# hmmscan :: search sequence(s) against a profile database
# HMMER 3.1b1 (May 2013); http://hmmer.org/
# Copyright (C) 2013 Howard Hughes Medical Institute.
# Freely distributed under the GNU General Public License (GPLv3).
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# query sequence file:             prot_multi.fa
# target HMM database:             /home/bow/db/hmmer/protdb/Pfam-A.hmm
# output directed to file:         hmmscan/text_31b1_hmmscan_001.out
# per-seq hits tabular output:     hmmscan/tab_31b1_hmmscan_001.out
# per-dom hits tabular output:     hmmscan/domtab_31b1_hmmscan_001.out
# pfam-style tabular hit output:   hmmscan/pfamtab_31b1_hmmscan_001.out
# number of worker threads:        2
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       random_s00  [L=22]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (22 residues searched)
Target model(s):                       14831  (2610332 nodes)
Passed MSV filter:                        57  (0.0038433); expected 296.6 (0.02)
Passed bias filter:                       44  (0.00296676); expected 296.6 (0.02)
Passed Vit filter:                         1  (6.74263e-05); expected 14.8 (0.001)
Passed Fwd filter:                         0  (0); expected 0.1 (1e-05)
Initial search space (Z):              14831  [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: 00:00:03.04
# Mc/sec: 18.89
//
Query:       gi|4885477|ref|NP_005359.1|  [L=154]
Description: myoglobin [Homo sapiens]
Scores for 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   80.5   0.3    1.6e-22   79.8   0.3    1.3  1  Globin    Globin


Domain annotation for each model (and alignments):
>> Globin  Globin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   79.8   0.3   1.1e-26   1.6e-22       1     109 [.       7     112 ..       7     113 .. 0.97

  Alignments for each domain:
  == domain 1  score: 79.8 bits;  conditional E-value: 1.1e-26
                                  HHHHHHHHHHHHHTHHHHHHHHHHHHHHHHSGGGGGGSTTTTTTT-HHHHCTSHHHHHHHHHHHHHHHHHHHTTTSHHHHHH CS
                       Globin   1 dkalvkaswekvkanaeelgaeilkrlFkaypdtkklFkkfgdlssaedlksspkfkahakkvlaalgeavknldndealka 82 
                                  +++lv   w+kv+a+++ +g+e+l rlFk +p+t ++F kf++l+s +++k s+++k+h+++vl+alg ++k+   ++ ++a
  gi|4885477|ref|NP_005359.1|   7 EWQLVLNVWGKVEADIPGHGQEVLIRLFKGHPETLEKFDKFKHLKSEDEMKASEDLKKHGATVLTALGGILKK---KGHHEA 85 
                                  5789*********************************************************************...689*** PP

                                  HHHHHHHHHHTSTT--HHHHHHHHHHH CS
                       Globin  83 alkklaarHaergkvdpanFklfgeal 109
                                   +k la++Ha+++k++ ++ + ++e++
  gi|4885477|ref|NP_005359.1|  86 EIKPLAQSHATKHKIPVKYLEFISECI 112
                                  ************************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (154 residues searched)
Target model(s):                       14831  (2610332 nodes)
Passed MSV filter:                       494  (0.0333086); expected 296.6 (0.02)
Passed bias filter:                      402  (0.0271054); expected 296.6 (0.02)
Passed Vit filter:                        35  (0.00235992); expected 14.8 (0.001)
Passed Fwd filter:                         1  (6.74263e-05); expected 0.1 (1e-05)
Initial search space (Z):              14831  [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: 00:00:03.72
# Mc/sec: 108.06
//
Query:       gi|126362951|ref|NP_001075106.1|  [L=106]
Description: leukocyte immunoglobulin-like receptor subfamily B member 1 isoform 2 precursor [Homo sapiens]
Scores for 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-10   38.8   0.4    1.4e-09   38.3   0.4    1.3  1  Ig_3      Immunoglobulin domain
    1.6e-06   28.1   0.1      2e-06   27.8   0.1    1.1  1  Ig_2      Immunoglobulin domain


Domain annotation for each model (and alignments):
>> Ig_3  Immunoglobulin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.3   0.4   1.8e-13   1.4e-09       1      73 [.       8      83 ..       8      87 .. 0.95

  Alignments for each domain:
  == domain 1  score: 38.3 bits;  conditional E-value: 1.8e-13
                              Ig_3  1 kPvisvspsptvtsggnvtLtCsaeggpppptisWy.....ietppelqgsegssssestLtissvtsedsGtYtCva 73
                                      kP++s++psp+v+sggnv L+C ++     + +s +     +++   +++++ ++ss +++++ +v+++ +  Y+C+a
  gi|126362951|ref|NP_001075106.1|  8 KPTLSAQPSPVVNSGGNVILQCDSQVA--FDGFSLCkegedEHPQCLNSQPHARGSSRAIFSVGPVSPSRRWWYRCYA 83
                                      8************************99..78888888****************************************9 PP

>> Ig_2  Immunoglobulin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.8   0.1   2.6e-10     2e-06       1      80 []       8     103 ..       8     103 .. 0.75

  Alignments for each domain:
  == domain 1  score: 27.8 bits;  conditional E-value: 2.6e-10
                              Ig_2   1 kpvlsapp.tvvtegenvtLtCqapgnptpkvqwykdg.....eelsqsqna.......lfipnvsaedsGtYtCra 64 
                                       kp+lsa+p +vv+ g nv L C ++   ++ +++ k+g     + l++++ a       + +  vs++    Y+C+a
  gi|126362951|ref|NP_001075106.1|   8 KPTLSAQPsPVVNSGGNVILQCDSQVA-FDGFSLCKEGedehpQCLNSQPHArgssraiFSVGPVSPSRRWWYRCYA 83 
                                       799**9997779*************86.9*******98643333333333335555553444669************ PP

                              Ig_2  65 ....snsegskqsnsvevtv 80 
                                           s +e+s +s+ +e+ v
  gi|126362951|ref|NP_001075106.1|  84 ydsnSPYEWSLPSDLLELLV 103
                                       88554455699999999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (106 residues searched)
Target model(s):                       14831  (2610332 nodes)
Passed MSV filter:                       171  (0.0115299); expected 296.6 (0.02)
Passed bias filter:                      140  (0.00943969); expected 296.6 (0.02)
Passed Vit filter:                        11  (0.00074169); expected 14.8 (0.001)
Passed Fwd filter:                         2  (0.000134853); expected 0.1 (1e-05)
Initial search space (Z):              14831  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.31u 0.24s 00:00:00.55 Elapsed: 00:00:01.22
# Mc/sec: 226.80
//
Query:       gi|22748937|ref|NP_065801.1|  [L=1204]
Description: exportin-5 [Homo sapiens]
Scores for 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  116.6   7.8    1.2e-33  116.1   4.9    2.8  2  Xpo1      Exportin 1-like protein
     0.0044   16.9   0.0      0.036   13.9   0.0    2.7  2  IBN_N     Importin-beta N-terminal domain
  ------ inclusion threshold ------
      0.095   11.7   0.3        1.3    8.0   0.3    2.3  2  Rac1      Rac1-binding domain


Domain annotation for each model (and alignments):
>> Xpo1  Exportin 1-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  116.1   4.9   2.3e-37   1.2e-33       2     148 .]     110     271 ..     109     271 .. 0.98
   2 ?   -1.8   0.0      0.52   2.6e+03     112     139 ..     499     525 ..     496     529 .. 0.86

  Alignments for each domain:
  == domain 1  score: 116.1 bits;  conditional E-value: 2.3e-37
                                   HHHHHHHHHHHHHHHHHHTTTTSTTHHHHHHHHHCT-HHHHHHHHHHHHHHHHHHCTSXTTCSHHHHHHHHHHHHHHHHHH CS
                          Xpo1   2 kflrnklaealaelflqeypnqWpsffddllsllssspsglelllriLkvlpeEiadfsrskleqerrnelkdllrsqvqk 82 
                                   +++++ l+++++e++++e+p++Wp+++ +l  l++++++++el++ iL++l+e++++f  ++l  +rr++++++l++++++
  gi|22748937|ref|NP_065801.1| 110 NHIKDALSRIVVEMIKREWPQHWPDMLIELDTLSKQGETQTELVMFILLRLAEDVVTF--QTLPPQRRRDIQQTLTQNMER 188
                                   89******************************************************99..79******************* PP

                                   HHHHHHHHHHHHHHCC...............HHHHHHHHHHHHHHHTTTS-HHHHHSSC..HHHHHHHHTTSCCCHHHHHH CS
                          Xpo1  83 ilelllqileqsvskk...............sselveatLkclsswvswidiglivnsp..llsllfqlLndpelreaAve 146
                                   i+++ll+ l+++v+k+               ++++  a+L++l+ +++w+++++i +++  ll++l+ lLn++el+  A+e
  gi|22748937|ref|NP_065801.1| 189 IFSFLLNTLQENVNKYqqvktdtsqeskaqaNCRVGVAALNTLAGYIDWVSMSHITAENckLLEILCLLLNEQELQLGAAE 269
                                   **************99*****************************************8889******************** PP

                                   HH CS
                          Xpo1 147 cL 148
                                   cL
  gi|22748937|ref|NP_065801.1| 270 CL 271
                                   *8 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 0.52
                                   HHTTTS-HHHHHSSCHHHHHHHHTTSCC CS
                          Xpo1 112 swvswidiglivnspllsllfqlLndpe 139
                                   s+v+w  ++l+++s +++ +f+ Ln++e
  gi|22748937|ref|NP_065801.1| 499 SFVQWEAMTLFLES-VITQMFRTLNREE 525
                                   899*********98.8888899998776 PP

>> IBN_N  Importin-beta N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.9   0.0   7.3e-06     0.036       4      75 ..      36      98 ..      33     100 .. 0.87
   2 ?   -3.5   0.0         2     1e+04      57      74 ..     168     185 ..     165     186 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 7.3e-06
                                  HHHHHHHSTTHHHHHHHHHHHTTTSTHHHHHHHHHHHHHHHHHSCCHHHHHHHHCSSHHHHHHHHHHHHHHH CS
                         IBN_N  4 qLnqlekqkPgflsallqilanksldlevRqlAalyLknlItkhWkseeaqrqqqlpeeekelIrnnllnll 75
                                   ++++++  P ++++ l+++ +k+    vR++++++L++ ++ +W+         ++  ek +++n++ +l+
  gi|22748937|ref|NP_065801.1| 36 FCEEFKEKCPICVPCGLRLA-EKTQVAIVRHFGLQILEHVVKFRWN--------GMSRLEKVYLKNSVMELI 98
                                  56788886699*********.6555899******************........999999****99999887 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 2
                                   HCSSHHHHHHHHHHHHHH CS
                         IBN_N  57 qqlpeeekelIrnnllnl 74 
                                   q+lp++ + +I ++l + 
  gi|22748937|ref|NP_065801.1| 168 QTLPPQRRRDIQQTLTQN 185
                                   6899*******9999876 PP

>> Rac1  Rac1-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0   0.3   0.00026       1.3      94     171 ..      89     169 ..      82     254 .. 0.75
   2 ?    0.8   0.0     0.041     2e+02     150     181 ..     310     341 ..     296     354 .. 0.82

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.00026
                          Rac1  94 qlrsnimksvvepslkriqkqldqshslvdia..slerar.khletllevlvtlsqqgekvssevydflyrlaevkvslsv 171
                                   +l++ +m  +++ +l+ ++++     +l+ i    ++r   +h   +l  l tls+qge  +  v  +l rlae  v++  
  gi|22748937|ref|NP_065801.1|  89 YLKNSVMELIANGTLNILEEENHIKDALSRIVveMIKREWpQHWPDMLIELDTLSKQGETQTELVMFILLRLAEDVVTFQT 169
                                   788899999******9998766666666666511555543499*9*****************999999******9888642 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.041
                          Rac1 150 kvssevydflyrlaevkvslsvrldtlkqqqe 181
                                    +  + y fl+rl +v  +l+ +l +l + + 
  gi|22748937|ref|NP_065801.1| 310 GLVEKHYVFLKRLCQVLCALGNQLCALLGADS 341
                                   556678******************99977665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1204 residues searched)
Target model(s):                       14831  (2610332 nodes)
Passed MSV filter:                       567  (0.0382307); expected 296.6 (0.02)
Passed bias filter:                      414  (0.0279145); expected 296.6 (0.02)
Passed Vit filter:                        32  (0.00215764); expected 14.8 (0.001)
Passed Fwd filter:                         3  (0.000202279); expected 0.1 (1e-05)
Initial search space (Z):              14831  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.78u 0.28s 00:00:01.06 Elapsed: 00:00:03.60
# Mc/sec: 873.01
//
Query:       gi|125490392|ref|NP_038661.2|  [L=352]
Description: POU domain, class 5, transcription factor 1 isoform 1 [Mus musculus]
Scores for 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-37  124.8   0.5    1.5e-36  123.9   0.5    1.5  1  Pou          Pou domain - N-terminal to homeobox domain
    1.8e-18   65.8   1.1    3.4e-18   64.9   1.1    1.5  1  Homeobox     Homeobox domain
  ------ inclusion threshold ------
      0.013   15.6   0.0       0.18   12.0   0.0    2.2  2  HTH_31       Helix-turn-helix domain
      0.043   13.5   0.0        0.1   12.2   0.0    1.6  1  Homeobox_KN  Homeobox KN domain
       0.15   10.5   0.1       0.28    9.6   0.1    1.4  1  DUF521       Protein of unknown function (DUF521)


Domain annotation for each model (and alignments):
>> Pou  Pou domain - N-terminal to homeobox domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  123.9   0.5     5e-40   1.5e-36       3      75 .]     133     205 ..     131     205 .. 0.97

  Alignments for each domain:
  == domain 1  score: 123.9 bits;  conditional E-value: 5e-40
                            Pou   3 eldleeleefakefkqrrikLgltqadvgsalgalyGkefsqttIcrFEalqLslknmckLkpllekWLeeae 75 
                                    ++ ++ele+fak +kq+ri+Lg+tqadvg +lg+l+Gk+fsqttIcrFEalqLslknmckL+pllekW+eea+
  gi|125490392|ref|NP_038661.2| 133 KALQKELEQFAKLLKQKRITLGYTQADVGLTLGVLFGKVFSQTTICRFEALQLSLKNMCKLRPLLEKWVEEAD 205
                                    67899******************************************************************96 PP

>> Homeobox  Homeobox domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   64.9   1.1   1.2e-21   3.4e-18       1      57 []     224     280 ..     224     280 .. 0.98

  Alignments for each domain:
  == domain 1  score: 64.9 bits;  conditional E-value: 1.2e-21
                                    TT--SS--HHHHHHHHHHHHHSSS--HHHHHHHHHHCTS-HHHHHHHHHHHHHHHHC CS
                       Homeobox   1 rrkRttftkeqleeLeelFeknrypsaeereeLAkklgLterqVkvWFqNrRakekk 57 
                                    +rkRt++++     Le++F k+++ps ++++++A++lgL++++V+vWF+NrR+k k+
  gi|125490392|ref|NP_038661.2| 224 KRKRTSIENRVRWSLETMFLKCPKPSLQQITHIANQLGLEKDVVRVWFCNRRQKGKR 280
                                    79****************************************************997 PP

>> HTH_31  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   5.9e-05      0.18       1      35 [.     141     181 ..     141     185 .. 0.95
   2 ?    0.9   0.0      0.18   5.3e+02      39      62 ..     245     268 ..     243     270 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 5.9e-05
                         HTH_31   1 aLGarLralReraGLsqeevAerag......vSastlsriE 35 
                                    +++ +L++ R + G +q++v+  +g      +S++t++r E
  gi|125490392|ref|NP_038661.2| 141 QFAKLLKQKRITLGYTQADVGLTLGvlfgkvFSQTTICRFE 181
                                    7999**************************99*******99 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.18
                         HTH_31  39 rgrpslavlaalaralgldeaera 62 
                                    ++ psl++++ +a+ lgl+ + ++
  gi|125490392|ref|NP_038661.2| 245 CPKPSLQQITHIANQLGLEKDVVR 268
                                    678**************9988765 PP

>> Homeobox_KN  Homeobox KN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   3.5e-05       0.1       7      39 ..     244     276 ..     241     277 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 3.5e-05
                    Homeobox_KN   7 hnPYPskevkeelakqTglsrkqidnWFiNaRr 39 
                                    + P Ps +++  +a+q gl  + +  WF N R 
  gi|125490392|ref|NP_038661.2| 244 KCPKPSLQQITHIANQLGLEKDVVRVWFCNRRQ 276
                                    56779*************************996 PP

>> DUF521  Protein of unknown function (DUF521)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   0.1   9.4e-05      0.28     273     334 ..     221     280 ..     197     294 .. 0.77

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 9.4e-05
                         DUF521 273 adlaavleelnkakkeevdlvvlGcPhlsleeleelaellkgrkkkvsvelvvttsravlsk 334
                                    + +++ + +++++   +++ ++l cP  sl++++++a++l  +k    v+++ +  r+  ++
  gi|125490392|ref|NP_038661.2| 221 QARKRKRTSIENRVRWSLETMFLKCPKPSLQQITHIANQLGLEK--DVVRVWFCNRRQKGKR 280
                                    345666667778888899************************99..9999999988876554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (352 residues searched)
Target model(s):                       14831  (2610332 nodes)
Passed MSV filter:                       663  (0.0447037); expected 296.6 (0.02)
Passed bias filter:                      493  (0.0332412); expected 296.6 (0.02)
Passed Vit filter:                        45  (0.00303419); expected 14.8 (0.001)
Passed Fwd filter:                         5  (0.000337132); expected 0.1 (1e-05)
Initial search space (Z):              14831  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.43u 0.33s 00:00:00.76 Elapsed: 00:00:04.08
# Mc/sec: 225.21
//
[ok]
