# hmmscan :: search sequence(s) against a profile HMM database
# HMMER 3.0b2 (June 2009); http://hmmer.org/
# Copyright (C) 2009 Howard Hughes Medical Institute.
# Freely distributed under the GNU General Public License (GPLv3).
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# query sequence file:             /home/niguts/usr08/shisakam/FASTA/gib_24355.fasta
# target HMM database:             /home/niguts/usr08/shisakam/PFAM/ver24.0/Pfam-A.hmm
# sequence search space set to:    100000
# set reporting thresholds to:     GA cutoffs
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       ABE38168.1  [L=249]
Description: rpal2 ABE38168.1 GIB00345CH01 "electron transfer flavoprotein beta-subunit"
Scores for complete 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-39  137.5   2.1    3.3e-39  136.9   1.5    1.2  1  PF01012  Electron transfer flavoprotein domain
  ------ inclusion threshold ------
        2.3   11.3   0.1         34    7.6   0.0    2.4  2  PF03477  ATP cone domain
        2.6   10.8   0.0        6.1    9.6   0.0    1.6  1  PF03652  Uncharacterised protein family (UPF0081)
        3.5   10.1   0.1         16    8.0   0.0    2.0  1  PF09183  Domain of unknown function (DUF1947)
         12    8.1   0.4         49    6.1   0.0    2.1  1  PF10145  Phage-related minor tail protein
         15    7.9   0.3         35    6.8   0.2    1.6  1  PF02817  e3 binding domain
         56    5.8   0.0    1.2e+02    4.7   0.0    1.6  1  PF03543  Yersinia/Haemophilus virulence surface antigen
         57    5.9   0.0    1.4e+02    4.7   0.0    1.6  1  PF11087  Protein of unknown function (DUF2881)
         62    6.2   0.0    1.2e+02    5.2   0.0    1.5  1  PF00679  Elongation factor G C-terminus
         69    6.0   0.3    1.2e+02    5.3   0.2    1.4  1  PF10562  Calmodulin-binding domain C0 of NMDA receptor NR1 s
         78    5.2   0.0    1.2e+02    4.5   0.0    1.2  1  PF12134  PRP8 domain IV core
         96    4.8   0.0    2.4e+02    3.6   0.0    1.5  1  PF08744  Plant transcription factor NOZZLE
         98    5.1   0.2    5.4e+02    2.6   0.0    2.0  1  PF01168  Alanine racemase, N-terminal domain
    1.1e+02    5.4   0.3    2.3e+02    4.3   0.0    1.8  1  PF11112  Pyocin activator protein PrtN
    1.1e+02    2.8   0.2    1.4e+02    2.5   0.1    1.2  1  PF04465  Protein of unknown function (DUF499)
    1.4e+02    5.2   0.0    4.7e+02    3.5   0.0    1.8  1  PF05413  Putative closterovirus papain-like endopeptidase
    1.7e+02    2.8   0.1    2.5e+02    2.3   0.1    1.2  1  PF00463  Isocitrate lyase family
    4.9e+02    2.4   0.1    7.2e+02    1.9   0.1    1.1  1  PF06912  Protein of unknown function (DUF1275)
    7.4e+02    1.0   0.0    1.2e+03    0.4   0.0    1.2  1  PF00982  Glycosyltransferase family 20


Domain and alignment annotation for each model:
>> PF01012  Electron transfer flavoprotein domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  136.9   1.5   6.2e-43   3.3e-39      10     164 .]      32     183 ..      25     183 .. 0.96

  Alignments for each domain:
  == domain 1    score: 136.9 bits;  conditional E-value: 6.2e-43
                 CCEE-CHHHHHHHHHHHHHHHS.SSEEEEEE---GGGGHHHHHHHHH-----EEEEEE-GGCS-.-CCCHHHHHHHHHHHH--SEEEEESSTTTT-... CS
     PF01012  10 egklnpvdlealeaArrlaekl.ggevtalvvGpveeaaealrealaamGadevllledpalagydpeatakalaalikkekpdlvllgatstgkd... 104
                 ++++np+d+ a+e+A+rl+e++  +ev+++++Gp ++a e+lr+ la mGad+ +l++ +     +p+a+ak+l+a++ +e+p l++lg++++++d   
  ABE38168.1  32 KMSMNPFDEIAVEEALRLKEAGkATEVVVVSIGP-AQASETLRTGLA-MGADRGILVKAEGTV--EPLAVAKILKAIADEEQPGLIILGKQAIDDDsnq 126
                 789******************9555*********.************.*********999776..9********************************* PP

                 -HHHHHHHHT--EEEEEEEEEE---EEEEEEE--TTSCEEEEESS--SEEEEE-TTSS-- CS
     PF01012 105 laprlAalLgtplitdvteleaeggkltvtRpieggnavvtvklpdrpavltvrpgafep 164
                 ++++lAalLg++++t +++le+eg+ +tv R+++gg+++v++k p   a++t++ +++ep
  ABE38168.1 127 TGQMLAALLGWAQATFASKLEVEGSDFTVSREVDGGSQTVKLKGP---AIVTTDLRLNEP 183
                 *********************************************...*********998 PP

>> PF03477  ATP cone domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6   0.0    0.0064        34       4      24 ..      86     106 ..      84     126 .. 0.88
   2 ?    0.8   0.0      0.82   4.3e+03      42      66 ..     216     241 ..     214     245 .. 0.86

  Alignments for each domain:
  == domain 1    score: 7.6 bits;  conditional E-value: 0.0064
     PF03477   4 iKRdgrvepfdvekIkraiek 24 
                 +K  g+vep+ v kI +ai+ 
  ABE38168.1  86 VKAEGTVEPLAVAKILKAIAD 106
                 6889***************85 PP

  == domain 2    score: 0.8 bits;  conditional E-value: 0.82
     PF03477  42 evekeledkkee.gisteeIqdlvek 66 
                 ev k++e ++++ g++++++ +lv k
  ABE38168.1 216 EVLKTVEPSGRKaGVKVKDVAELVSK 241
                 78888888888899*****9999975 PP

>> PF03652  Uncharacterised protein family (UPF0081)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   0.0    0.0012       6.1      12      60 ..      73     118 ..      70     154 .. 0.83

  Alignments for each domain:
  == domain 1    score: 9.6 bits;  conditional E-value: 0.0012
     PF03652  12 riGvAvsdelgilaspletierkskkkdleelkelvkeeevdeiVvGlP 60 
                 r+G+A++  +gil ++  t+e     + ++ lk++++ee++  i++G  
  ABE38168.1  73 RTGLAMGADRGILVKAEGTVEPL---AVAKILKAIADEEQPGLIILGKQ 118
                 89******************977...78999999*************65 PP

>> PF09183  Domain of unknown function (DUF1947)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0   0.0    0.0029        16       9      34 ..     195     219 ..     191     223 .. 0.86

  Alignments for each domain:
  == domain 1    score: 8.0 bits;  conditional E-value: 0.0029
                 HHHHHHHHHHT.----------EEEE CS
     PF09183   9 dakeliskvkekygidlsgeklEvgk 34 
                  +k + +k +++yg+dl   +lEv k
  ABE38168.1 195 KKKPIAEKTADQYGVDLAP-RLEVLK 219
                 57899************99.999976 PP

>> PF10145  Phage-related minor tail protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   0.0    0.0094        49      85     128 ..     202     245 ..     199     247 .. 0.89

  Alignments for each domain:
  == domain 1    score: 6.1 bits;  conditional E-value: 0.0094
     PF10145  85 yaanngattvkdmaealkqvgavakalGlsgeetaallaalaqa 128
                 ++a++++++++   e+lk v + ++++G++++++a l + l + 
  ABE38168.1 202 KTADQYGVDLAPRLEVLKTVEPSGRKAGVKVKDVAELVSKLKNE 245
                 68899999999999**********************99998875 PP

>> PF02817  e3 binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   0.2    0.0066        35       7      37 ..     198     235 ..     193     237 .. 0.89

  Alignments for each domain:
  == domain 1    score: 6.8 bits;  conditional E-value: 0.0066
                 HHHHHHHHHTT--GG.......G---------BCHHHH CS
     PF02817   7 PaaRkLAaekgidLs.......qvkGTGpgGRItkeDV 37 
                 P a k A + g+dL+        v+++G++  +  +DV
  ABE38168.1 198 PIAEKTADQYGVDLAprlevlkTVEPSGRKAGVKVKDV 235
                 889999**********************9988888888 PP

>> PF03543  Yersinia/Haemophilus virulence surface antigen
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   0.0     0.023   1.2e+02      84     134 ..      54     115 ..      16     122 .. 0.80

  Alignments for each domain:
  == domain 1    score: 4.7 bits;  conditional E-value: 0.023
                 HH..HHHHH---EE-S--EEEE.............----------HHHHHH-----EEEEEE CS
     PF03543  84 qatdtwlkeaglepseeelklg...........evagavsaenvsrllkaildtgsdgllvl 134
                 +at+ ++ + g+ + +e+l+ g           +++g+v+   v ++lkai+d+++ gl++l
  ABE38168.1  54 KATEVVVVSIGPAQASETLRTGlamgadrgilvKAEGTVEPLAVAKILKAIADEEQPGLIIL 115
                 7788888888888888888888999999999999********************99998876 PP

>> PF11087  Protein of unknown function (DUF2881)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   0.0     0.026   1.4e+02      21      35 ..     235     249 .]     228     249 .] 0.85

  Alignments for each domain:
  == domain 1    score: 4.7 bits;  conditional E-value: 0.026
     PF11087  21 lAvlvsrrsntAGvi 35 
                 +A lvs+  n AGvi
  ABE38168.1 235 VAELVSKLKNEAGVI 249
                 789***********9 PP

>> PF00679  Elongation factor G C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2   0.0     0.023   1.2e+02      46      70 ..       2      26 ..       1      39 [. 0.91

  Alignments for each domain:
  == domain 1    score: 5.2 bits;  conditional E-value: 0.023
     PF00679 46 eaevPlaeligysteLrslTsGrgs 70
                +  vP++ +++y+ ++r  + G g+
  ABE38168.1  2 KVLVPVKRVVDYNVKIRVKSDGSGV 26
                6789******************996 PP

>> PF10562  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 ?    5.3   0.2     0.022   1.2e+02       8      23 ..     191     206 ..     190     207 .. 0.91

  Alignments for each domain:
  == domain 1    score: 5.3 bits;  conditional E-value: 0.022
     PF10562   8 gaKeKqmELArkAaDk 23 
                 + K K++ +A k+aD 
  ABE38168.1 191 IMKAKKKPIAEKTADQ 206
                 6899**********95 PP

>> PF12134  PRP8 domain IV core
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5   0.0     0.023   1.2e+02      86     111 ..      97     122 ..      83     131 .. 0.87

  Alignments for each domain:
  == domain 1    score: 4.5 bits;  conditional E-value: 0.023
     PF12134  86 vaalirslPkeeqPkkiivtrkalld 111
                 va +++++  eeqP+ ii+ ++a+ d
  ABE38168.1  97 VAKILKAIADEEQPGLIILGKQAIDD 122
                 77899***************999877 PP

>> PF08744  Plant transcription factor NOZZLE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6   0.0     0.045   2.4e+02      23      86 ..      54     117 ..      45     134 .. 0.83

  Alignments for each domain:
  == domain 1    score: 3.6 bits;  conditional E-value: 0.045
     PF08744  23 rntrlvvnssgeirtetkksrgrkpgsktaqqkqkkptlrgmgvaklerfiieeekkklvvatv 86 
                 + t +vv s g  ++      g   g+  +   + + t+  + vak+ + i++ee+  l++ ++
  ABE38168.1  54 KATEVVVVSIGPAQASETLRTGLAMGADRGILVKAEGTVEPLAVAKILKAIADEEQPGLIILGK 117
                 5688888899988887666779999999999999*********************998876554 PP

>> PF01168  Alanine racemase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6   0.0       0.1   5.4e+02     103     139 ..     211     247 ..     197     249 .] 0.80

  Alignments for each domain:
  == domain 1    score: 2.6 bits;  conditional E-value: 0.1
                 TSS-EEEEEBE--SSS----SHHHHHHHHHHHHCSTT CS
     PF01168 103 agrplrvhlkvdtgmeRlGvepeeaeelaealaalpg 139
                    +l+v+  v+ ++ + Gv++++++el+ +l+++ g
  ABE38168.1 211 LAPRLEVLKTVEPSGRKAGVKVKDVAELVSKLKNEAG 247
                 5578889999999999******88*******997655 PP

>> PF11112  Pyocin activator protein PrtN
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3   0.0     0.044   2.3e+02      57      75 ..     228     246 ..     199     247 .. 0.85

  Alignments for each domain:
  == domain 1    score: 4.3 bits;  conditional E-value: 0.044
     PF11112  57 kfVkvedLAayideraeeA 75 
                  +Vkv+d+A+++++ ++eA
  ABE38168.1 228 AGVKVKDVAELVSKLKNEA 246
                 69*********99988877 PP

>> PF04465  Protein of unknown function (DUF499)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5   0.1     0.027   1.4e+02     843     874 ..       2      33 ..       1      63 [. 0.87

  Alignments for each domain:
  == domain 1    score: 2.5 bits;  conditional E-value: 0.027
     PF04465 843 evrvkvkplgderikvelssnfselesdevsl 874
                 +v v vk++ d+++k++++s++s +e  +v++
  ABE38168.1   2 KVLVPVKRVVDYNVKIRVKSDGSGVELTNVKM 33 
                 677999********************999998 PP

>> PF05413  Putative closterovirus papain-like endopeptidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.5   0.0     0.089   4.7e+02      54      78 ..      11      35 ..       6      39 .. 0.88

  Alignments for each domain:
  == domain 1    score: 3.5 bits;  conditional E-value: 0.089
     PF05413 54 eayeikvevegdcglvevgsiglsl 78
                 +y++k+ v+ d   ve+ ++ +s+
  ABE38168.1 11 VDYNVKIRVKSDGSGVELTNVKMSM 35
                57*****************999987 PP

>> PF00463  Isocitrate lyase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3   0.1     0.048   2.5e+02     199     228 ..       2      31 ..       1      35 [. 0.92

  Alignments for each domain:
  == domain 1    score: 2.3 bits;  conditional E-value: 0.048
                 -EE--HHHHHHHHHHHHHHHHH-----EEE CS
     PF00463 199 kvlvpiqehinrlvairlaadilgsdlllv 228
                 kvlvp++  ++  v ir++ d  g++l  v
  ABE38168.1   2 KVLVPVKRVVDYNVKIRVKSDGSGVELTNV 31 
                 8********************999998765 PP

>> PF06912  Protein of unknown function (DUF1275)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.9   0.1      0.14   7.2e+02      28      50 ..     124     146 ..     123     151 .. 0.90

  Alignments for each domain:
  == domain 1    score: 1.9 bits;  conditional E-value: 0.14
     PF06912  28 shqTGntvllglalaggnfalal 50 
                 s+qTG ++   l++a+  fa++l
  ABE38168.1 124 SNQTGQMLAALLGWAQATFASKL 146
                 89**************9998776 PP

>> PF00982  Glycosyltransferase family 20
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   0.0      0.22   1.2e+03     410     434 ..      23      47 ..      19      56 .. 0.88

  Alignments for each domain:
  == domain 1    score: 0.4 bits;  conditional E-value: 0.22
                 --TTT-TTS.EEE-TT-HHHHHHHH CS
     PF00982 410 GaaqsLkdaailvNPwdieevaeai 434
                 G+  +L+++ +  NP+d  +v+ea+
  ABE38168.1  23 GSGVELTNVKMSMNPFDEIAVEEAL 47 
                 7788999999*********999997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (249 residues)
Target model(s):                       11912  (2158902 nodes)
Passed MSV filter:                       323  (0.0271155); expected 238.2 (0.02)
Passed bias filter:                      270  (0.0226662); expected 238.2 (0.02)
Passed Vit filter:                        19  (0.00159503); expected 11.9 (0.001)
Passed Fwd filter:                        19  (0.00159503); expected 0.1 (1e-05)
Initial search space (Z):             100000  [as set by --Z on cmdline]
Domain search space  (domZ):              19  [number of targets reported over threshold]
# CPU time: 0.19u 0.06s 00:00:00.25 Elapsed: 00:00:00
# Mc/sec: 2829.30
//