# 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_9001.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:       BAB80017.1  [L=262]
Description: cper0 etfB.1 GIB00075CH01 "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
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      8e-40  138.9   0.0    9.8e-40  138.6   0.0    1.1  1  PF01012  Electron transfer flavoprotein domain
  ------ inclusion threshold ------
       0.29   14.2   0.7         28    7.8   0.1    2.7  2  PF02302  PTS system, Lactose/Cellobiose specific IIB subunit
         30    7.3   0.0         64    6.3   0.0    1.5  1  PF06029  AlkA N-terminal domain
         72    6.0   0.0    1.4e+02    5.1   0.0    1.4  1  PF07237  Protein of unknown function (DUF1428)
    1.1e+02    4.6   0.0    1.5e+02    4.2   0.0    1.2  1  PF10339  Velum formation protein
    1.3e+02    4.9   0.0    2.4e+02    4.0   0.0    1.3  1  PF01288  7,8-dihydro-6-hydroxymethylpterin-pyrophosphokinase
    1.4e+02    4.7   0.2    2.7e+02    3.8   0.1    1.5  1  PF08970  Sporulation inhibitor A
    2.4e+02    4.3   0.0    5.9e+02    3.1   0.0    1.7  1  PF07453  NUMOD1 domain
    2.4e+02    4.1   0.0    5.5e+02    2.9   0.0    1.5  1  PF11835  Domain of unknown function (DUF3355)
    3.2e+02    3.9   0.0    6.5e+02    2.9   0.0    1.4  1  PF09286  Pro-kumamolisin, activation domain
    3.3e+02    3.3   0.0    7.4e+02    2.1   0.0    1.5  1  PF08452  DNA polymerase family B exonuclease domain, N-termi
    3.9e+02    3.5   0.7    7.1e+02    2.7   0.1    1.7  1  PF11538  Snurportin1
    5.5e+02    2.9   0.2    1.1e+03    1.9   0.1    1.5  1  PF00831  Ribosomal L29 protein
    5.8e+02    2.8   0.0    1.2e+03    1.8   0.0    1.4  1  PF06463  Molybdenum Cofactor Synthesis C
    2.7e+03    0.4   0.0    2.9e+03    0.3   0.0    1.3  1  PF02167  Cytochrome C1 family


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 !  138.6   0.0   1.5e-43   9.8e-40       4     164 .]      24     185 ..      21     185 .. 0.97

  Alignments for each domain:
  == domain 1    score: 138.6 bits;  conditional E-value: 1.5e-43
                 EE-GCC.CCEE-CHHHHHHHHHHHHHHHSSSEEEEEE---GGGGHHHHHHHHH-----EEEEEE-GGCS-.-CCCHHHHHHHHHHH.H--SEEEEESST CS
     PF01012   4 vlaehg.egklnpvdlealeaArrlaeklggevtalvvGpveeaaealrealaamGadevllledpalagydpeatakalaalikk.ekpdlvllgats 100
                 vl ++g ++k+np+dl+ale A+r++ek+gg + ++++Gp ++a++ ++ea++ mGade  l++d+++ag+d +at+++l++ +kk  ++d++l+g+++
  BAB80017.1  24 VLKRDGvDSKMNPYDLYALETALRIKEKKGGNIKVISMGP-PQAKAVIKEAYS-MGADEGTLVSDRKFAGADVLATSYTLSQGVKKcGDFDIILCGKQT 120
                 7889999*********************************.************.********************************888********** PP

                 TTT-...-HHHHHHHHT--EEEEEE.EEEE---EEEEEEE--TTSCEEEEESS--SEEEEE-TTSS-- CS
     PF01012 101 tgkd...laprlAalLgtplitdvt.eleaeggkltvtRpieggnavvtvklpdrpavltvrpgafep 164
                 t++d   ++p +A++Lg+p++++v   l+++++ + v+  + +  +v++vk p   ++ltv++++f+p
  BAB80017.1 121 TDGDtaqVGPEMAEYLGIPHVANVRrILDVNDDFIKVEMDMPNTIEVLEVKYP---CLLTVDKDIFQP 185
                 *************************8889999989******************...**********98 PP

>> PF02302  PTS system, Lactose/Cellobiose specific IIB subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.8   0.1    0.0042        28      29      89 ..      16      71 ..       7      72 .. 0.79
   2 ?    4.1   0.0     0.064   4.2e+02      45      80 ..     108     137 ..      89     152 .. 0.68

  Alignments for each domain:
  == domain 1    score: 7.8 bits;  conditional E-value: 0.0042
     PF02302 29 ieaegeaga..eleaeeiaddaDlvllapqvkykdlarfagkpvavipikdaigimdgekvlk 89
                +e+  ++g+  ++ ++ +++ +Dl+ l + +++   +++ g +++vi++ +     ++++v+k
  BAB80017.1 16 VEVDEKTGVlkRDGVDSKMNPYDLYALETALRI--KEKKGG-NIKVISMGP----PQAKAVIK 71
                777778888887788889999***********7..555555.699999988....77888877 PP

  == domain 2    score: 4.1 bits;  conditional E-value: 0.064
     PF02302  45 addaDlvllapqvkykdlarfagkpvavipikdaig 80 
                   d+D++l+++q++ +    ++g p     +++++g
  BAB80017.1 108 CGDFDIILCGKQTT-DGDTAQVG-P----EMAEYLG 137
                 456**********9.45555555.3....3444444 PP

>> PF06029  AlkA N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   0.0    0.0096        64      74      96 ..     140     162 ..     125     175 .. 0.82

  Alignments for each domain:
  == domain 1    score: 6.3 bits;  conditional E-value: 0.0096
     PF06029  74 liarvrrllDLdadpeaIeaaLd 96 
                  +a+vrr+lD++ d  ++e  + 
  BAB80017.1 140 HVANVRRILDVNDDFIKVEMDMP 162
                 589***********999998873 PP

>> PF07237  Protein of unknown function (DUF1428)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   0.0     0.021   1.4e+02      41      79 ..     178     216 ..     165     222 .. 0.88

  Alignments for each domain:
  == domain 1    score: 5.1 bits;  conditional E-value: 0.021
     PF07237  41 wgddvpegkltsfkkavkakedEtvvfswiewpskatrd 79 
                 + +d+ + +l s+kk  ++ e E  v+s   +++k+++ 
  BAB80017.1 178 VDKDIFQPRLPSYKKKLETDEREINVISLNDFEDKDEKK 216
                 56688888999************************9875 PP

>> PF10339  Velum formation protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.2   0.0     0.023   1.5e+02      41      61 ..      78      98 ..      40     122 .. 0.87

  Alignments for each domain:
  == domain 1    score: 4.2 bits;  conditional E-value: 0.023
     PF10339 41 gtnatylgeksfigldvltes 61
                 +++t + ++ f+g+dvl+ s
  BAB80017.1 78 ADEGTLVSDRKFAGADVLATS 98
                4579**************987 PP

>> PF01288  7,8-dihydro-6-hydroxymethylpterin-pyrophosphokinase (HPPK)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.0   0.0     0.036   2.4e+02      91     115 ..     110     144 ..     102     148 .. 0.75

  Alignments for each domain:
  == domain 1    score: 4.0 bits;  conditional E-value: 0.036
                 --EEEEETT---B-SS..........-BSS-TTGG CS
     PF01288  91 DlDillyekevleeek..........LtiPhpeil 115
                 D Di+l++k++++ ++          L iPh    
  BAB80017.1 110 DFDIILCGKQTTDGDTaqvgpemaeyLGIPHVANV 144
                 99********9876554556666666999997655 PP

>> PF08970  Sporulation inhibitor A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.8   0.1      0.04   2.7e+02      19      28 ..     148     157 ..     146     160 .. 0.88

  Alignments for each domain:
  == domain 1    score: 3.8 bits;  conditional E-value: 0.04
                 TT--HHHHHH CS
     PF08970  19 LnLdpDFIeL 28 
                 L++++DFI++
  BAB80017.1 148 LDVNDDFIKV 157
                 89******86 PP

>> PF07453  NUMOD1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   0.0     0.088   5.9e+02      21      31 ..     131     141 ..     130     156 .. 0.87

  Alignments for each domain:
  == domain 1    score: 3.1 bits;  conditional E-value: 0.088
     PF07453  21 eAAkaLgishk 31 
                 e+A++Lgi h 
  BAB80017.1 131 EMAEYLGIPHV 141
                 89******995 PP

>> PF11835  Domain of unknown function (DUF3355)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.9   0.0     0.083   5.5e+02      19      33 ..     219     233 ..     215     237 .. 0.83

  Alignments for each domain:
  == domain 1    score: 2.9 bits;  conditional E-value: 0.083
     PF11835  19 aesTptalErVFpaT 33 
                 +++ pt++Er+Fp  
  BAB80017.1 219 LNGSPTQVERIFPPS 233
                 7999********975 PP

>> PF09286  Pro-kumamolisin, activation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.9   0.0     0.097   6.5e+02      33      63 ..     206     236 ..     202     244 .. 0.91

  Alignments for each domain:
  == domain 1    score: 2.9 bits;  conditional E-value: 0.097
     PF09286  33 lmdvsdPkspnygkhltaeevaelfapseet 63 
                 l+d  d + ++yg   ++ +v++ f ps+ +
  BAB80017.1 206 LNDFEDKDEKKYGLNGSPTQVERIFPPSNND 236
                 7899999********************9875 PP

>> PF08452  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 ?    2.1   0.0      0.11   7.4e+02       6      17 ..     206     217 ..     205     217 .. 0.92

  Alignments for each domain:
  == domain 1    score: 2.1 bits;  conditional E-value: 0.11
     PF08452   6 lNWFEnrGekrf 17 
                 lN FE + ek++
  BAB80017.1 206 LNDFEDKDEKKY 217
                 788*******98 PP

>> PF11538  Snurportin1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.7   0.1      0.11   7.1e+02       2      11 ..     185     194 ..     184     200 .. 0.82

  Alignments for each domain:
  == domain 1    score: 2.7 bits;  conditional E-value: 0.11
                 GGGCCTT-TT CS
     PF11538   2 PRlsqYKnkg 11 
                 PRl  YK k 
  BAB80017.1 185 PRLPSYKKKL 194
                 9******994 PP

>> PF00831  Ribosomal L29 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.9   0.1      0.17   1.1e+03       3      23 ..     239     259 ..     238     260 .. 0.87

  Alignments for each domain:
  == domain 1    score: 1.9 bits;  conditional E-value: 0.17
                 CCTTSHHHHHHHCCCCHHHHH CS
     PF00831   3 elrelsdeeLkeklkelkkeL 23 
                 e+ + +++eL e++++  +eL
  BAB80017.1 239 EIWTGDSSELSERMEDKLREL 259
                 788889999999999999998 PP

>> PF06463  Molybdenum Cofactor Synthesis C
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.8   0.0      0.18   1.2e+03      18      69 ..     183     234 ..     174     235 .. 0.86

  Alignments for each domain:
  == domain 1    score: 1.8 bits;  conditional E-value: 0.18
     PF06463  18 rekkfvsaaeildrleeklalradkketghparryrvssgegsvgiiapvsn 69 
                 ++ +++s+++ l++ e++++ ++ ++ ++++ ++y +++  ++v+ i p sn
  BAB80017.1 183 FQPRLPSYKKKLETDEREINVISLNDFEDKDEKKYGLNGSPTQVERIFPPSN 234
                 6677889999999999999999999999************9****9998777 PP

>> PF02167  Cytochrome C1 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.0      0.43   2.9e+03     122     160 ..     134     172 ..      57     244 .. 0.81

  Alignments for each domain:
  == domain 1    score: 0.3 bits;  conditional E-value: 0.43
                 ------TT----..----SS------S---S-SS-SS-- CS
     PF02167 122 gyeedpeavevreggyyNkyfpggviaMpkpLsdgqvey 160
                  y   p+ ++vr     N  f +  + Mp+ ++  +v+y
  BAB80017.1 134 EYLGIPHVANVRRILDVNDDFIKVEMDMPNTIEVLEVKY 172
                 566667777778888888888888888888887776654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (262 residues)
Target model(s):                       11912  (2158902 nodes)
Passed MSV filter:                       323  (0.0271155); expected 238.2 (0.02)
Passed bias filter:                      290  (0.0243452); expected 238.2 (0.02)
Passed Vit filter:                        16  (0.00134318); expected 11.9 (0.001)
Passed Fwd filter:                        15  (0.00125923); expected 0.1 (1e-05)
Initial search space (Z):             100000  [as set by --Z on cmdline]
Domain search space  (domZ):              15  [number of targets reported over threshold]
# CPU time: 0.20u 0.04s 00:00:00.24 Elapsed: 00:00:00
# Mc/sec: 2828.16
//