# 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.orf8.fasta
# target HMM database:             Pfam-A.hmm
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       BA000019.orf8  [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
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    6.7e-11   41.3   0.0    1.5e-09   37.0   0.0    2.5  2  HTH_AraC   Bacterial regulatory helix-turn-helix proteins, Ara
    3.8e-12   38.2  11.9    5.9e-08   25.0   2.5    2.9  2  PKSI-KS_m3 
      0.023   13.9   0.0       0.54    9.5   0.0    2.3  2  DUF746     Domain of Unknown Function (DUF746)

Domain annotation for each model (and alignments):
>> HTH_AraC  Bacterial regulatory helix-turn-helix proteins, AraC family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5   0.0     0.038   2.3e+02      10      36 ..     251     277 ..     242     278 .. 0.80
   2 !   37.0   0.0   2.6e-13   1.5e-09       8      41 ..     298     332 ..     295     333 .. 0.94

  Alignments for each domain:
  == domain 1    score: 1.5 bits;  conditional E-value: 0.038
                    -HHHHHHHHTS-HHHHHHHHHHH---- CS
       HTH_AraC  10 siadiAeevgfSpsyfsrlFkkytGvt 36 
                    s+ +++++vg++  +++r F+ ++  t
  BA000019.orf8 251 SLMELSRQVGLNDCTLKRGFRLVFDTT 277
                    66689999999999*******999877 PP

  == domain 2    score: 37.0 bits;  conditional E-value: 2.6e-13
                    .--HHHHHHHHTS.-HHHHHHHHHHH----HHHHH CS
       HTH_AraC   8 nwsiadiAeevgf.SpsyfsrlFkkytGvtPsqyr 41 
                    +++i++ A++vgf S+syf+++F+k++G++P++++
  BA000019.orf8 298 EINISQAARRVGFsSRSYFATAFRKKFGINPKEFL 332
                    5789*****************************97 PP

>> PKSI-KS_m3  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.0   2.5   3.6e-09   5.9e-08       1      16 []     538     553 ..     538     553 .. 0.99
   2 !   17.4   0.9     9e-07   1.5e-05       1      15 [.    1672    1686 ..    1672    1687 .. 0.96

  Alignments for each domain:
  == domain 1    score: 25.0 bits;  conditional E-value: 3.6e-09
      PKSI-KS_m3   1 GPSvtVDTACSSSLvA 16 
                     GPSvtVDT CSSSLvA
  AM746336.orf22 538 GPSVTVDTLCSSSLVA 553
                     9**************9 PP

  == domain 2    score: 17.4 bits;  conditional E-value: 9e-07
      PKSI-KS_m3    1 GPSvtVDTACSSSLv 15  
                      GP +++D ACSS Lv
  AM746336.orf22 1672 GPNLVIDSACSSALV 1686
                      9*************9 PP

>> DUF746  Domain of Unknown Function (DUF746)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   0.0   9.1e-05      0.54       4      32 ..     240     268 ..     237     275 .. 0.85
   2 ?    1.8   0.0     0.022   1.3e+02      13      28 ..     298     313 ..     293     319 .. 0.87

  Alignments for each domain:
  == domain 1    score: 9.5 bits;  conditional E-value: 9.1e-05
         DUF746   4 rllIrlLsqplslaeaadqlgtdegiiak 32 
                    + lIr L  p sl+e+++q+g+   + ++
  BA000019.orf8 240 EILIRNLENPPSLMELSRQVGLNDCTLKR 268
                    579******************98766655 PP

  == domain 2    score: 1.8 bits;  conditional E-value: 0.022
         DUF746  13 plslaeaadqlgtdeg 28 
                    ++ + +aa+++g +++
  BA000019.orf8 298 EINISQAARRVGFSSR 313
                    6899********9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (348 residues)
Target model(s):                       11912  (2158902 nodes)
Passed MSV filter:                       248  (0.0208193); expected 238.2 (0.02)
Passed bias filter:                      220  (0.0184688); expected 238.2 (0.02)
Passed Vit filter:                        19  (0.00159503); expected 11.9 (0.001)
Passed Fwd filter:                         2  (0.000167898); expected 0.1 (1e-05)
Initial search space (Z):              11912  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.24u 0.15s 00:00:00.39 Elapsed: 00:00:00.27
# Mc/sec: 2782.58
//
Query:       lcl|aorf_00010|P1  [L=132]
Description: IS481.original transposase
Scores for 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  130.0   0.4    3.8e-40  129.9   0.3    1.0  1  IS481.original.hmm  


Domain annotation for each model (and alignments):
>> IS481.original.hmm  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  129.9   0.3   6.6e-42   3.8e-40     127     281 ..       7     130 ..       2     132 .] 0.97

  Alignments for each domain:
  == domain 1    score: 129.9 bits;  conditional E-value: 6.6e-42
  IS481.original.hmm 127 kRYErdhPgeLvhmDvkklgripdgGgvkighRwrgrtrgrgkrtnqsrnrglgkayvitaiDDhSRfayaeilsd 202
                         +++E++hP +L+++D++++g+i + G+                            +y++t++D++S+   ++++++
   lcl|aorf_00010|P1   7 GEIETAHPSYLGSQDTFYVGNITGAGR----------------------------IYQQTFVDTYSKWDSTKLYTT 54 
                         579*******************88888............................********************* PP

  IS481.original.hmm 203 ettttaadfllraaayfygkigeeiitrvlTDnGaayrskkrsakhdFqealaelGIkhilTrprsPqTNGKiERF 278
                         +t++taad l++ ++ f+   ++++i r lTD+ ++y+sk   ++ d+  +la ++I+h++T++++PqTN ++ RF
   lcl|aorf_00010|P1  55 KTPITAADLLNDRVLSFFA-EQGMGIIRLLTDRSTEYCSKA--ETQDYELCLALNDIEHTKTKVYHPQTNDICRRF 127
                         *******************.********************8..********************************* PP

  IS481.original.hmm 279 hrT 281
                         h+ 
   lcl|aorf_00010|P1 128 HKA 130
                         *95 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (132 residues)
Target model(s):                         116  (57162 nodes)
Passed MSV filter:                         4  (0.0344828); expected 2.3 (0.02)
Passed bias filter:                        4  (0.0344828); expected 2.3 (0.02)
Passed Vit filter:                         3  (0.0258621); expected 0.1 (0.001)
Passed Fwd filter:                         1  (0.0172414); expected 0.0 (1e-05)
Initial search space (Z):                116  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.06u 0.00s 00:00:00.06 Elapsed: 00:00:00.06
# Mc/sec: 117.90
//
