# 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/broad_1734.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:       CIRT_00774  [L=714]
Description: cimm2 CIRG_00774 Broad_Institute ""
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
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.7e-14   54.6  11.8    8.5e-12   47.0   0.1    3.9  3  PF08159  NUC153 domain
  ------ inclusion threshold ------
        3.7    9.7   0.6         49    6.1   0.0    2.7  2  PF04911  ATP synthase j chain
          6    8.6   0.1         11    7.8   0.1    1.3  1  PF07401  Bovine Lentivirus VIF protein
        8.1    9.1   4.7         12    8.5   0.7    2.8  2  PF07904  CT20 family
         28    6.1   0.7         85    4.5   0.5    1.8  1  PF01905  CRISPR-associated negative autoregulator DevR/Csa2
         62    5.9   0.1    1.7e+02    4.6   0.1    1.7  1  PF07497  Rho termination factor, RNA-binding domain
         77    5.6   0.0    1.8e+02    4.4   0.0    1.6  1  PF02671  Paired amphipathic helix repeat
         95    4.9   0.9    2.4e+02    3.6   0.6    1.6  1  PF12184  De novo homeodomain
    1.7e+02    4.3   0.4    6.1e+02    2.5   0.1    2.0  1  PF07421  Neurotensin/neuromedin N precursor
    7.5e+02    2.9   0.1    1.5e+03    1.9   0.0    1.4  1  PF11420  Bacteriocin subtilosin A
      1e+03    0.4   2.9    5.1e+02    1.5   0.2    1.7  1  PF03063  Prismane/CO dehydrogenase family
    1.3e+03    2.2   0.0    3.9e+03    0.7   0.0    1.7  1  PF02202  Tachykinin family
    3.2e+03    1.2   0.8    7.2e+03    0.1   0.5    1.5  1  PF08111  Pea-VEAacid family
    4.8e+03    0.2   6.6      4e+04   -2.8   4.6    2.7  1  PF04408  Helicase associated domain (HA2)


Domain and alignment annotation for each model:
>> PF08159  NUC153 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6   0.1     0.094   6.7e+02       1      11 [.      29      39 ..      29      42 .. 0.82
   2 !    8.3   2.4    0.0016        11       1      13 [.      54      66 ..      54      67 .. 0.95
   3 !   47.0   0.1   1.2e-15   8.5e-12       1      30 []     626     655 ..     626     655 .. 0.98

  Alignments for each domain:
  == domain 1    score: 2.6 bits;  conditional E-value: 0.094
     PF08159  1 DpRFkalFedp 11
                DpRF+++  dp
  CIRT_00774 29 DPRFANIQSDP 39
                9****997777 PP

  == domain 2    score: 8.3 bits;  conditional E-value: 0.0016
     PF08159  1 DpRFkalFedpdF 13
                D RF+ +F d+dF
  CIRT_00774 54 DKRFAHMFHDKDF 66
                99*********** PP

  == domain 3    score: 47.0 bits;  conditional E-value: 1.2e-15
     PF08159   1 DpRFkalFedpdFaiDetspeFkklnpsek 30 
                 DpRF+ ++e++++aiD+t+p F+++ ++++
  CIRT_00774 626 DPRFQRIYESHEYAIDPTNPRFRQTDGMKA 655
                 9***************************95 PP

>> PF04911  ATP synthase j chain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.1   0.0      0.24   1.7e+03      28      48 ..     611     631 ..     608     635 .. 0.83
   2 ?    6.1   0.0    0.0069        49      32      48 ..     633     649 ..     630     654 .. 0.84

  Alignments for each domain:
  == domain 1    score: 1.1 bits;  conditional E-value: 0.24
     PF04911  28 adasmnsdEfknDPRnprakk 48 
                  +a m  d+fk D ++pr+++
  CIRT_00774 611 DEATMPVDDFKVDVKDPRFQR 631
                 5789999******99999984 PP

  == domain 2    score: 6.1 bits;  conditional E-value: 0.0069
     PF04911  32 mnsdEfknDPRnprakk 48 
                  +s E+  DP npr+++
  CIRT_00774 633 YESHEYAIDPTNPRFRQ 649
                 589************84 PP

>> PF07401  Bovine Lentivirus VIF protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.8   0.1    0.0015        11      11      48 ..      12      50 ..       4      64 .. 0.75

  Alignments for each domain:
  == domain 1    score: 7.8 bits;  conditional E-value: 0.0015
     PF07401 11 rrrgssnrrkrkaslistpaya.lypapryryprwefvr 48
                +rr +s+  k ++++i+ p +a +   pryr p  +  r
  CIRT_00774 12 KRRKTSSNDKADKDVITDPRFAnIQSDPRYRLPSKKHTR 50
                455566667888889999999768999*****9876655 PP

>> PF07904  CT20 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   0.7    0.0017        12      17      79 ..      52     113 ..      45     125 .. 0.76
   2 ?    0.5   0.1      0.52   3.7e+03      20      85 ..     585     616 ..     571     622 .. 0.52

  Alignments for each domain:
  == domain 1    score: 8.5 bits;  conditional E-value: 0.0017
     PF07904  17 GihkhFrmiciverlnsskeepklekeftaediwekLstlYnLekldeleealeesekeekrv 79 
                  i+k F  +   ++++++    +  ++++ +d +++L+++Y L+k d+ e + + + +ee+++
  CIRT_00774  52 KIDKRFAHMFHDKDFSRNAAVDRYGRKLRRDDTKKQLEKFYRLDK-DDVEGQISADDDEEVQK 113
                 5778887666677777777888999*******************9.67776777777777444 PP

  == domain 2    score: 0.5 bits;  conditional E-value: 0.52
     PF07904  20 khFrmiciverlnsskeepklekeftaediwekLstlYnLekldeleealeesekeekrvkdFtLP 85 
                 khF m  i +  ++ k++ k+                                   + ++ + t+P
  CIRT_00774 585 KHFDMNEIEKAQKRAKKAGKH----------------------------------RKGKKDEATMP 616
                 455554444444444332222..................................22344455555 PP

>> PF01905  CRISPR-associated negative autoregulator DevR/Csa2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5   0.5     0.012        85     203     226 ..     480     503 ..     472     511 .. 0.87

  Alignments for each domain:
  == domain 1    score: 4.5 bits;  conditional E-value: 0.012
     PF01905 203 kitskpvldenerkkRieaalkAl 226
                 ++++k++ +e+erk+R++a lkA 
  CIRT_00774 480 TTREKYIRKERERKQRRKAKLKAA 503
                 56789999**************96 PP

>> PF07497  Rho termination factor, RNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6   0.1     0.023   1.7e+02      36      75 ..      86     125 ..      83     128 .. 0.86

  Alignments for each domain:
  == domain 1    score: 4.6 bits;  conditional E-value: 0.023
     PF07497  36 sqirrfnLrtGDtveGkirsPkegeryfallkvekingee 75 
                 +q+ +f   + D veG+i +  ++e    ll+vek ++++
  CIRT_00774  86 KQLEKFYRLDKDDVEGQISADDDEEVQKELLRVEKEDYDP 125
                 588888888899*********************9977765 PP

>> PF02671  Paired amphipathic helix repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   0.0     0.026   1.8e+02      36      47 .]     189     200 ..     187     200 .. 0.94

  Alignments for each domain:
  == domain 1    score: 4.4 bits;  conditional E-value: 0.026
     PF02671  36 pdLleeFneFLp 47 
                 +dL+  F++FLp
  CIRT_00774 189 EDLMAVFSSFLP 200
                 8**********9 PP

>> PF12184  De novo homeodomain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6   0.6     0.034   2.4e+02      12      20 ..     564     572 ..     555     572 .. 0.84

  Alignments for each domain:
  == domain 1    score: 3.6 bits;  conditional E-value: 0.034
     PF12184  12 tSAAeRAEl 20 
                  SAA RAEl
  CIRT_00774 564 ASAAQRAEL 572
                 6*******8 PP

>> PF07421  Neurotensin/neuromedin N precursor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5   0.1     0.085   6.1e+02     129     169 .]     246     286 ..     237     286 .. 0.88

  Alignments for each domain:
  == domain 1    score: 2.5 bits;  conditional E-value: 0.085
     PF07421 129 gndknekeevikrkipyilkrqlyenkprrpyilkrgsyyy 169
                 + d +e ee ik+ i      q ++    r y l r  y+y
  CIRT_00774 246 AGDDEEEEEKIKQAILKEDEGQDFDSTQLRKYQLERLRYFY 286
                 4577889999*****999999******************98 PP

>> PF11420  Bacteriocin subtilosin A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.9   0.0      0.22   1.5e+03      17      30 ..     448     461 ..     446     463 .. 0.92

  Alignments for each domain:
  == domain 1    score: 1.9 bits;  conditional E-value: 0.22
                 -----S-------- CS
     PF11420  17 GPiPDFEiAGAtGL 30 
                 GP+ D E+  A GL
  CIRT_00774 448 GPVGDMEVTFAAGL 461
                 9**********998 PP

>> PF03063  Prismane/CO dehydrogenase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5   0.2     0.071   5.1e+02      39     102 ..     562     623 ..     552     653 .. 0.79

  Alignments for each domain:
  == domain 1    score: 1.5 bits;  conditional E-value: 0.071
                 --HHHHHHHHHHHHHHHHHHCGGGSTTT--SHHHHHHHHHHHHHHHHHHSHHHHHHHHHHHHHH CS
                 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
     PF03063  39 glaahaahareladtlilkalfktltnvnfddeeklkalaealgieeelsieelakevaevale 102
                 g+a+ a+  r+ ++ l+++ + +t++ +++++ ek ++ a++ g + +++++e    v +++++
  CIRT_00774 562 GAASAAQ--RAELELLMMDDKTSTIKHFDMNEIEKAQKRAKKAGKHRKGKKDEATMPVDDFKVD 623
                 4444444..4556799****************************99999777776666666554 PP

>> PF02202  Tachykinin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   0.0      0.54   3.9e+03       3       8 ..     344     349 ..     344     349 .. 0.93

  Alignments for each domain:
  == domain 1    score: 0.7 bits;  conditional E-value: 0.54
                 TCHHH- CS
     PF02202   3 kPdqFv 8  
                 kP++Fv
  CIRT_00774 344 KPNEFV 349
                 8****8 PP

>> PF08111  Pea-VEAacid family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   0.5         1   7.2e+03       9      15 .]     240     246 ..     238     246 .. 0.93

  Alignments for each domain:
  == domain 1    score: 0.1 bits;  conditional E-value: 1
     PF08111   9 VDSYVEA 15 
                 VDS VEA
  CIRT_00774 240 VDSDVEA 246
                 9*****9 PP

>> PF04408  Helicase associated domain (HA2)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   4.6       5.6     4e+04      52      90 ..     460     498 ..     453     613 .. 0.76

  Alignments for each domain:
  == domain 1    score: -2.8 bits;  conditional E-value: 5.6
     PF04408  52 tivallsvdsiflnpdkkkenaekdnaknklikearrkl 90 
                  + a+   ds+f+n+ +k+e + ++  +++ ++++rrk+
  CIRT_00774 460 GLTAAPARDSVFENEPEKEETTREKYIRKERERKQRRKA 498
                 566777779999995555555553333333333333332 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (714 residues)
Target model(s):                       11912  (2158902 nodes)
Passed MSV filter:                       889  (0.0746306); expected 238.2 (0.02)
Passed bias filter:                      191  (0.0160343); expected 238.2 (0.02)
Passed Vit filter:                        25  (0.00209872); expected 11.9 (0.001)
Passed Fwd filter:                        21  (0.00176293); expected 0.1 (1e-05)
Initial search space (Z):             100000  [as set by --Z on cmdline]
Domain search space  (domZ):              14  [number of targets reported over threshold]
# CPU time: 0.43u 0.04s 00:00:00.47 Elapsed: 00:00:00
# Mc/sec: 3584.78
//