# 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_28341.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:       ACF56764.1  [L=64]
Description: spne4 ACF56764.1 GIB00761CH01 "conserved hypothetical protein"
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
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
        1.2   11.6   0.0        1.5   11.3   0.0    1.2  1  PF01330  RuvA N terminal domain
        5.4    9.6   0.0        5.7    9.5   0.0    1.1  1  PF10998  Protein of unknown function (DUF2838)
         10    9.1   0.1         11    9.0   0.1    1.1  1  PF06575  Protein of unknown function (DUF1132)
         13    8.3   0.2         19    7.7   0.2    1.3  1  PF06970  Replication initiator protein A (RepA) N-terminus
         14    8.3   0.0         17    8.0   0.0    1.3  1  PF03937  Protein of unknown function (DUF339)
         15    7.8   0.0         16    7.7   0.0    1.0  1  PF02576  Uncharacterised BCR, YhbC family COG0779
         17    7.7   0.0         16    7.8   0.0    1.0  1  PF11150  Protein of unknown function (DUF2927)
         27    7.0   0.1         30    6.8   0.0    1.0  1  PF09223  YodA
         28    7.2   0.1         32    7.0   0.1    1.1  1  PF07166  Protein of unknown function (DUF1398)
         47    6.7   0.0         49    6.6   0.0    1.1  1  PF03711  Orn/Lys/Arg decarboxylase, C-terminal domain
         63    6.2   0.1    1.4e+02    5.1   0.0    1.6  1  PF10902  Protein of unknown function (DUF2693)
         79    6.0   0.1    1.3e+02    5.3   0.1    1.3  1  PF07659  Domain of Unknown Function (DUF1599)
    1.1e+02    5.1   0.0    1.4e+02    4.7   0.0    1.2  1  PF01067  Calpain large subunit, domain III
    1.4e+02    5.4   0.2    1.7e+02    5.1   0.2    1.2  1  PF10273  Pre-rRNA-processing protein TSR2
    2.4e+02    4.3   0.1    3.4e+02    3.9   0.1    1.3  1  PF02723  Non-structural protein NS3/Small envelope protein E
    3.3e+02    4.0   0.0    6.3e+02    3.1   0.0    1.4  1  PF02202  Tachykinin family
    3.7e+02    3.8   0.1    5.5e+02    3.3   0.0    1.3  1  PF07835  Bacterial aa3 type cytochrome c oxidase subunit IV
    6.5e+02    2.5   0.4    9.4e+02    2.0   0.3    1.3  1  PF08047  Histidine operon leader peptide
    1.1e+03    2.9   1.4    2.2e+03    1.9   1.0    1.5  1  PF07391  NPR nonapeptide repeat (2 copies)


Domain and alignment annotation for each model:
>> PF01330  RuvA N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00028       1.5      29      57 ..      26      54 ..      13      56 .. 0.85

  Alignments for each domain:
  == domain 1    score: 11.3 bits;  conditional E-value: 0.00028
                E--HHHHCTS-------BB-EEEEETTEE CS
     PF01330 29 nvsentlaelpeegevklfthlivRedal 57
                n   +t+ el ee+e+ +f+ l+ +ed++
  ACF56764.1 26 NRVFKTNIELVEEKEADIFVGLVNKEDSK 54
                55557899*******************86 PP

>> PF10998  Protein of unknown function (DUF2838)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   0.0    0.0011       5.7      38      66 ..       1      30 [.       1      49 [. 0.83

  Alignments for each domain:
  == domain 1    score: 9.5 bits;  conditional E-value: 0.0011
     PF10998 38 mpirlytykkkklhyFllD.lCyflnalll 66
                m ir+  ++k+++  F l+ l+y++n ++ 
  ACF56764.1  1 MVIRVFDQQKNTYSSFALEeLSYYMNRVFK 30
                789*************9988******8765 PP

>> PF06575  Protein of unknown function (DUF1132)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   0.1    0.0021        11      29      65 ..       9      44 ..       3      59 .. 0.73

  Alignments for each domain:
  == domain 1    score: 9.0 bits;  conditional E-value: 0.0021
     PF06575 29 vkvvkeydvieefsyflnkrishniwkiyfsdesvif 65
                 k++ +   +ee+sy++n+  + ni ++    e++if
  ACF56764.1  9 QKNTYSSFALEELSYYMNRVFKTNIELVE-EKEADIF 44
                5666667789**************97765.3455555 PP

>> PF06970  Replication initiator protein A (RepA) N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   0.2    0.0037        19      43      74 ..       6      37 ..       4      39 .. 0.86

  Alignments for each domain:
  == domain 1    score: 7.7 bits;  conditional E-value: 0.0037
     PF06970 43 iDeegriYliftneelkellniskkkvikikk 74
                +D++++ Y  f  eel+ ++n   k+ i++++
  ACF56764.1  6 FDQQKNTYSSFALEELSYYMNRVFKTNIELVE 37
                79***************999988777777766 PP

>> PF03937  Protein of unknown function (DUF339)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0   0.0    0.0032        17      10      43 ..      20      53 ..      10      54 .. 0.90

  Alignments for each domain:
  == domain 1    score: 8.0 bits;  conditional E-value: 0.0032
                HHHHH---HHHHHHHH--HHHHHHHHHHHTS-HH CS
     PF03937 10 ElDllLgrFadkhletlseeeldaferLLdleDp 43
                El + + r ++ ++e  +e+e d f  L + eD+
  ACF56764.1 20 ELSYYMNRVFKTNIELVEEKEADIFVGLVNKEDS 53
                788888888999*******************997 PP

>> PF02576  Uncharacterised BCR, YhbC family COG0779
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   0.0     0.003        16      51     102 ..       4      55 ..       1      61 [. 0.91

  Alignments for each domain:
  == domain 1    score: 7.7 bits;  conditional E-value: 0.003
                 GGTTTS----S-EEEEEE-----S--SSHHHH------EEEB---S-SSS-S CS
     PF02576  51 alLdaedpiseeYtLeVsSPGleRpLkteedfarfkGekvkvslkeeiegrk 102
                 +++d++++  ++++Le  S  ++R +kt+ ++ + k   + v l ++ ++++
  ACF56764.1   4 RVFDQQKNTYSSFALEELSYYMNRVFKTNIELVEEKEADIFVGLVNKEDSKR 55 
                 789**9**************************************99888765 PP

>> PF11150  Protein of unknown function (DUF2927)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.8   0.0     0.003        16      40      88 ..       8      53 ..       1      63 [. 0.77

  Alignments for each domain:
  == domain 1    score: 7.8 bits;  conditional E-value: 0.003
     PF11150 40 gvapadraedlelveselarLarvtgldislasdkeanltvlfvsedei 88
                +++ ++ + +le+++ +++   rv + +i+l+++kea+++v +v++++ 
  ACF56764.1  8 QQKNTYSSFALEELSYYMN---RVFKTNIELVEEKEADIFVGLVNKEDS 53
                4666777777888866665...999*******************99984 PP

>> PF09223  YodA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   0.0    0.0057        30      42      82 ..       4      44 ..       2      62 .. 0.76

  Alignments for each domain:
  == domain 1    score: 6.8 bits;  conditional E-value: 0.0057
     PF09223 42 evlekkaekkkkktaeeykeyyekGyktdverikiedktvt 82
                +v++++ ++ ++ + ee   y ++ +kt++e ++ ++  + 
  ACF56764.1  4 RVFDQQKNTYSSFALEELSYYMNRVFKTNIELVEEKEADIF 44
                5899999999999999**9999*********9988776653 PP

>> PF07166  Protein of unknown function (DUF1398)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0   0.1    0.0061        32      20      53 ..      11      44 ..       2      55 .. 0.79

  Alignments for each domain:
  == domain 1    score: 7.0 bits;  conditional E-value: 0.0061
                HHHHHHHHH-SSEEEEETTTS-EEEE-SSS-EEE CS
     PF07166 20 lfyselkrhnvsyyiyylatenikivlendevvl 53
                  ys +  +++syy+  +   ni++v e++  + 
  ACF56764.1 11 NTYSSFALEELSYYMNRVFKTNIELVEEKEADIF 44
                4467777889****************99876655 PP

>> PF03711  Orn/Lys/Arg decarboxylase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6   0.0    0.0094        49       4      31 ..       5      32 ..       3      58 .. 0.78

  Alignments for each domain:
  == domain 1    score: 6.6 bits;  conditional E-value: 0.0094
                HHHHTCCCCTT-BHHHHHHHHHHHHHHC CS
     PF03711  4 lvaesperYegltlreLcqeihdlyken 31
                ++++++++Y+++ l eL+  + +++k+n
  ACF56764.1  5 VFDQQKNTYSSFALEELSYYMNRVFKTN 32
                6889999**************9999876 PP

>> PF10902  Protein of unknown function (DUF2693)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   0.0     0.027   1.4e+02      51      69 ..       3      21 ..       1      26 [. 0.92

  Alignments for each domain:
  == domain 1    score: 5.1 bits;  conditional E-value: 0.027
     PF10902 51 vrvydvelkawRsFrldkl 69
                +rv+d + + + sF l+ l
  ACF56764.1  3 IRVFDQQKNTYSSFALEEL 21
                89*************9987 PP

>> PF07659  Domain of Unknown Function (DUF1599)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   0.1     0.025   1.3e+02      35      52 ..      32      49 ..      22      50 .. 0.86

  Alignments for each domain:
  == domain 1    score: 5.3 bits;  conditional E-value: 0.025
     PF07659 35 ketlVdEgiksefidiiN 52
                + +lV+E + + f++++N
  ACF56764.1 32 NIELVEEKEADIFVGLVN 49
                4589*************9 PP

>> PF01067  Calpain large subunit, domain III
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   0.0     0.027   1.4e+02      26      58 ..      22      54 ..       8      60 .. 0.84

  Alignments for each domain:
  == domain 1    score: 4.7 bits;  conditional E-value: 0.027
     PF01067 26 tfltNPqfrlslkepddedctvliaLmqknrrk 58
                ++ +N  f+ +++  ++++  +++ L+ k+ +k
  ACF56764.1 22 SYYMNRVFKTNIELVEEKEADIFVGLVNKEDSK 54
                7999****9999999999999*****9877654 PP

>> PF10273  Pre-rRNA-processing protein TSR2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   0.2     0.032   1.7e+02      40      72 ..       2      34 ..       1      40 [. 0.90

  Alignments for each domain:
  == domain 1    score: 5.1 bits;  conditional E-value: 0.032
     PF10273 40 vvelftsnkevdqedieelLlqvmldeFevnve 72
                v+ +f ++k+++++   e L  +m+  F +n+e
  ACF56764.1  2 VIRVFDQQKNTYSSFALEELSYYMNRVFKTNIE 34
                78899999999988888889**********998 PP

>> PF02723  Non-structural protein NS3/Small envelope protein E
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.9   0.1     0.064   3.4e+02      56      71 ..       3      19 ..       2      30 .. 0.80

  Alignments for each domain:
  == domain 1    score: 3.9 bits;  conditional E-value: 0.064
     PF02723 56 vkvYdrgkqlyksym.e 71
                ++v+d+ k+ y+s+  e
  ACF56764.1  3 IRVFDQQKNTYSSFAlE 19
                789**********9754 PP

>> PF02202  Tachykinin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   0.0      0.12   6.3e+02       5      10 ..      42      47 ..      41      47 .. 0.85

  Alignments for each domain:
  == domain 1    score: 3.1 bits;  conditional E-value: 0.12
                HHH--- CS
     PF02202  5 dqFvGL 10
                d FvGL
  ACF56764.1 42 DIFVGL 47
                66***9 PP

>> PF07835  Bacterial aa3 type cytochrome c oxidase subunit IV
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.3   0.0       0.1   5.5e+02      12      21 ..       7      16 ..       6      18 .. 0.87

  Alignments for each domain:
  == domain 1    score: 3.3 bits;  conditional E-value: 0.1
     PF07835 12 aehEkTYegF 21
                +++++TY +F
  ACF56764.1  7 DQQKNTYSSF 16
                589*****99 PP

>> PF08047  Histidine operon leader peptide
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0   0.3      0.18   9.4e+02       1       4 [.      25      28 ..      25      31 .. 0.85

  Alignments for each domain:
  == domain 1    score: 2.0 bits;  conditional E-value: 0.18
     PF08047  1 MnRV 4 
                MnRV
  ACF56764.1 25 MNRV 28
                ***9 PP

>> PF07391  NPR nonapeptide repeat (2 copies)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.9   1.0      0.42   2.2e+03       1       5 [.      34      38 ..      34      39 .. 0.61

  Alignments for each domain:
  == domain 1    score: 1.9 bits;  conditional E-value: 0.42
     PF07391  1 ElVEE 5 
                ElVEE
  ACF56764.1 34 ELVEE 38
                56666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (64 residues)
Target model(s):                       11912  (2158902 nodes)
Passed MSV filter:                       457  (0.0383647); expected 238.2 (0.02)
Passed bias filter:                      412  (0.034587); expected 238.2 (0.02)
Passed Vit filter:                        19  (0.00159503); expected 11.9 (0.001)
Passed Fwd filter:                        19  (0.00159503); expected 0.1 (1e-05)
Initial search space (Z):             100000  [as set by --Z on cmdline]
Domain search space  (domZ):              19  [number of targets reported over threshold]
# CPU time: 0.12u 0.04s 00:00:00.16 Elapsed: 00:00:00
# Mc/sec: 1151.41
//