# hmmscan :: search sequence(s) against a profile database
# HMMER 3.0 (March 2010); http://hmmer.org/
# Copyright (C) 2010 Howard Hughes Medical Institute.
# Freely distributed under the GNU General Public License (GPLv3).
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# query sequence file:             BA000019.orf1.fasta
# target HMM database:             /data/biodata/HMMerDB/Pfam.hmm
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       BA000019.orf1  [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
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      6e-30  105.2   0.3    6.7e-30  105.0   0.2    1.0  1  Peripla_BP_2    Periplasmic binding protein
  ------ inclusion threshold ------
      0.036   14.7   0.0       0.09   13.4   0.0    1.7  1  DUF2726         Protein of unknown function (DUF2726)
      0.039   14.1   0.3      0.049   13.8   0.2    1.1  1  Pfam-B_1590     
       0.22   12.5   0.0       0.33   12.0   0.0    1.3  1  Pfam-B_6580     
       0.25   12.1   0.2       0.37   11.5   0.2    1.2  1  Calpain_III     Calpain large subunit, domain III
       0.42   11.5   1.2        1.7    9.5   0.1    2.3  3  MHCassoc_trimer Class II MHC-associated invariant chain trim
        1.2    9.2   2.2        1.3    9.1   1.5    1.1  1  DUF3498         Domain of unknown function (DUF3498)


Domain annotation for each model (and alignments):
>> Peripla_BP_2  Periplasmic binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  105.0   0.2   1.5e-33   6.7e-30      59     236 ..       2     173 ..       1     175 [. 0.93

  Alignments for each domain:
  == domain 1    score: 105.0 bits;  conditional E-value: 1.5e-33
   Peripla_BP_2  59 lkPDlvivsafgalvseieellelgipvvavessstaeslleqirllgellgeedeaeelvaelesridavkaridsl.kpktvlvfgyadegikv 153
                    lkPDl+i+ +++   ++i+++l++ +p+v v+  s+  s+++ +r ++++l+ee++++ + +++++ri+++++r  +  ++ +v+v+g+++ +ik+
  BA000019.orf1   2 LKPDLIIGREYQ---KNIYNQLSNFAPTVLVDWGSF-TSFQDNFRYIAQVLNEEEQGKLVLQQYQKRIRDLQDRMGERlQKIEVSVIGFSGQSIKS 93 
                    8***********...********************9.*****************************************999999999999997777 PP

   Peripla_BP_2 154 vfgsgswvgdlldaaggeni.iaeakgseseeisaEqilaadpdviivsgrgedtktgveelkenplwaelpAvkngrvyllds 236
                    ++  +  ++++ld+ag++ i i++++++ + eis+E+++++d+dv++v       k+ +   ++nplw +l+Avk+++vy++++
  BA000019.orf1  94 LNR-DAVFNQVLDDAGIKRIsIQKNQQERYLEISIENLNKYDADVLFVINE---SKEQLYPDLKNPLWHHLRAVKKQQVYVVNQ 173
                    776.5678999999****99777777*************************...77777777899***************9976 PP

>> DUF2726  Protein of unknown function (DUF2726)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0     2e-05      0.09      79     112 ..      86     119 ..      79     130 .. 0.75

  Alignments for each domain:
  == domain 1    score: 13.4 bits;  conditional E-value: 2e-05
        DUF2726  79 ashkqgkaekrDalkeealekAgipllrvkakks 112
                    +s ++ k  +rDa+++++l+ Agi+ + +++ ++
  BA000019.orf1  86 FSGQSIKSLNRDAVFNQVLDDAGIKRISIQKNQQ 119
                    4555777999****************99954433 PP

>> Pfam-B_1590  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.2   1.1e-05     0.049       6     102 ..      78     169 ..      74     195 .. 0.75

  Alignments for each domain:
  == domain 1    score: 13.8 bits;  conditional E-value: 1.1e-05
    Pfam-B_1590   6 risafinlfiGqsvsrktivnail.slleqkGflkrswnkinlpctyvnlsieriskfdflpilskikgkeisyklyGeteWqtidklLlnvnkhk 100
                    +i   +  f Gqs++  +  +a++  +l++ G  + s +k n    y+++sie+++k+d   ++   + ke +y  + +  W+++      v+k++
  BA000019.orf1  78 KIEVSVIGFSGQSIKSLNR-DAVFnQVLDDAGIKRISIQK-NQQERYLEISIENLNKYDADVLFVINESKEQLYPDLKNPLWHHLR----AVKKQQ 167
                    5666666789999876554.34441578999999999988.56789*************98888888899****999999997654....444444 PP

    Pfam-B_1590 101 af 102
                    ++
  BA000019.orf1 168 VY 169
                    44 PP

>> Pfam-B_6580  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   7.2e-05      0.33      36      89 ..      70     124 ..      61     139 .. 0.83

  Alignments for each domain:
  == domain 1    score: 12.0 bits;  conditional E-value: 7.2e-05
    Pfam-B_6580  36 ewLedrlataaaAalvldalqseelpr.alqrelLeaigakavvlrkdqtrrlla 89 
                    +++ +rl+++++  +   +   + l+r a+ +++L+ +g+k + ++k+q+ r l 
  BA000019.orf1  70 DRMGERLQKIEVSVIGFSGQSIKSLNRdAVFNQVLDDAGIKRISIQKNQQERYLE 124
                    5677889999999999999988888862699******************999764 PP

>> Calpain_III  Calpain large subunit, domain III
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.2   8.1e-05      0.37      25      91 ..      35     102 ..      31     129 .. 0.75

  Alignments for each domain:
  == domain 1    score: 11.5 bits;  conditional E-value: 8.1e-05
    Calpain_III  25 etfltNPqfrlslkepddedctvliaLmqknrrkkrkk.geenltigfavykv.kkkekeldkeffkkn 91 
                     +f +N  +  ++ +++++  +++++ +qk+ r ++   ge++  i+++v+   +++ k+l+++++ ++
  BA000019.orf1  35 TSFQDNFRYIAQVLNEEEQ-GKLVLQQYQKRIRDLQDRmGERLQKIEVSVIGFsGQSIKSLNRDAVFNQ 102
                    48999**********9987.7999999999988776655888888999998887777788888766555 PP

>> MHCassoc_trimer  Class II MHC-associated invariant chain trimerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.5   0.0       4.3     2e+04      41      49 ..      29      37 ..      27      41 .. 0.78
   2 ?    0.1   0.0      0.35   1.6e+03       4      36 ..      51      81 ..      49      96 .. 0.74
   3 ?    9.5   0.1   0.00038       1.7       9      43 ..     139     176 ..     131     178 .. 0.73

  Alignments for each domain:
  == domain 1    score: -3.5 bits;  conditional E-value: 4.3
                     HHHHHHHHH CS
  MHCassoc_trimer 41 vdWksfEsW 49
                     vdW sf s+
    BA000019.orf1 29 VDWGSFTSF 37
                     689999886 PP

  == domain 2    score: 0.1 bits;  conditional E-value: 0.35
                     HHHHHHHHHHH-TT---------HHHHHHHHHH CS
  MHCassoc_trimer  4 edqvkhLllksdPkkvfPqlketlleNLksLKk 36
                     e+q k  l++ +  k   +l++ + e L+++  
    BA000019.orf1 51 EEQGKLVLQQYQ--KRIRDLQDRMGERLQKIEV 81
                     556666677777..7789999999999998765 PP

  == domain 3    score: 9.5 bits;  conditional E-value: 0.00038
                      HHHHHH-TT---------HHHHHHHHHHH....S-HHHH CS
  MHCassoc_trimer   9 hLllksdPkkvfPqlketlleNLksLKkt....mdevdW 43 
                        + +s+ ++++P+lk+ l + L++ Kk+    ++++dW
    BA000019.orf1 139 FVINESK-EQLYPDLKNPLWHHLRAVKKQqvyvVNQSDW 176
                      5556666.899****************973443456666 PP

>> DUF3498  Domain of unknown function (DUF3498)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1   1.5   0.00029       1.3     395     425 ..      43      73 ..      35     137 .. 0.81

  Alignments for each domain:
  == domain 1    score: 9.1 bits;  conditional E-value: 0.00029
                    ------------------------------- CS
        DUF3498 395 yErRLlsQeeQaqklLleYqaRLedseeRLR 425
                    y +  l  eeQ + +L++Yq+R+ d ++R+ 
  BA000019.orf1  43 YIAQVLNEEEQGKLVLQQYQKRIRDLQDRMG 73 
                    66788999*****************999984 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (198 residues)
Target model(s):                       31912  (6698792 nodes)
Passed MSV filter:                      1891  (0.0592567); expected 638.2 (0.02)
Passed bias filter:                     1237  (0.0387628); expected 638.2 (0.02)
Passed Vit filter:                       100  (0.00313362); expected 31.9 (0.001)
Passed Fwd filter:                         7  (0.000219353); expected 0.3 (1e-05)
Initial search space (Z):              31912  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.74u 0.55s 00:00:01.29 Elapsed: 00:00:07.01
# Mc/sec: 189.21
//
Query:       lcl|Test_ID.1|P1  [L=463]
Description: 281521..282909 
Scores for complete 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   19.9   1.5    4.3e-06   18.9   1.0    1.4  1  IS4.original 
    2.3e-06   19.7   1.5    4.3e-06   18.8   1.0    1.4  1  IS4.original 


Domain annotation for each model (and alignments):
>> IS4.original  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   1.0   8.9e-08   4.3e-06     315     353 ..     335     369 ..     318     391 .. 0.75

  Alignments for each domain:
  == domain 1    score: 18.9 bits;  conditional E-value: 8.9e-08
      IS4.original 315 filatnlddeldaediaelYrlRwqiElfFrelKsllgl 353
                         lat+  +el+ae+i+ lY +Rw+iE +F+ lK   ++
  lcl|Test_ID.1|P1 335 LLLATE--TELSAEEILRLYARRWGIEPLFHNLKR--WW 369
                       345555..**************************7..44 PP

>> IS4.original  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   1.0     9e-08   4.3e-06     315     353 ..     335     369 ..     318     391 .. 0.75

  Alignments for each domain:
  == domain 1    score: 18.8 bits;  conditional E-value: 9e-08
      IS4.original 315 filatnlddeldaediaelYrlRwqiElfFrelKsllgl 353
                         lat+  +el+ae+i+ lY +Rw+iE +F+ lK   ++
  lcl|Test_ID.1|P1 335 LLLATE--TELSAEEILRLYARRWGIEPLFHNLKR--WW 369
                       345555..**************************7..44 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (463 residues)
Target model(s):                          96  (37031 nodes)
Passed MSV filter:                        16  (0.166667); expected 1.9 (0.02)
Passed bias filter:                       16  (0.166667); expected 1.9 (0.02)
Passed Vit filter:                         9  (0.09375); expected 0.1 (0.001)
Passed Fwd filter:                         2  (0.0208333); expected 0.0 (1e-05)
Initial search space (Z):                 96  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.03u 0.02s 00:00:00.04 Elapsed: 00:00:00.06
# Mc/sec: 276.54
//
