# 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_20637.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:       AAL63125.1  [L=471]
Description: paer1 AAL63125.1 GIB00076CH01 "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
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.2e-21   78.2   0.0    2.2e-20   76.1   0.0    2.0  1  PF04055  Radical SAM superfamily
    2.5e-05   26.8   0.1    0.00011   24.8   0.0    2.1  1  PF00583  Acetyltransferase (GNAT) family
  ------ inclusion threshold ------
        4.8    9.2   0.0        7.6    8.5   0.0    1.2  1  PF02145  Rap/ran-GAP
        8.6    9.1   0.0         20    7.9   0.0    1.6  1  PF03454  MoeA C-terminal region (domain IV)
        9.9    8.1   0.0         22    7.0   0.0    1.5  1  PF07081  Protein of unknown function (DUF1349)
         37    6.4   0.0         94    5.1   0.0    1.6  1  PF04909  Amidohydrolase
         39    6.7   0.0         66    6.0   0.0    1.3  1  PF11905  Domain of unknown function (DUF3425)
         43    6.6   0.2    4.1e+02    3.4   0.0    2.2  2  PF08992  Quinohemoprotein amine dehydrogenase, gamma subunit
         59    6.7   0.1    9.5e+02    3.0   0.0    2.7  1  PF07661  MORN repeat variant
    1.5e+02    3.5   0.0      2e+02    3.1   0.0    1.1  1  PF08101  Domain of unknown function (DUF1708)
    1.5e+02    3.4   0.2    2.1e+02    2.9   0.1    1.1  1  PF06808  DctM-like transporters
    1.8e+02    4.3   1.3    5.4e+02    2.8   0.9    1.8  1  PF09005  Domain of unknown function (DUF1897)
    2.1e+02    4.2   0.0    4.1e+02    3.3   0.0    1.4  1  PF08844  Domain of unknown function (DUF1815)
    2.2e+02    4.6   0.0    4.9e+02    3.5   0.0    1.5  1  PF07659  Domain of Unknown Function (DUF1599)
    2.5e+02    4.1   0.0    6.3e+02    2.8   0.0    1.7  1  PF00880  Nebulin repeat
    3.1e+02    3.2   0.0      5e+02    2.5   0.0    1.2  1  PF12163  DNA replication regulator
    3.4e+02    3.6   0.0    7.6e+02    2.5   0.0    1.5  1  PF01303  Egg lysin (Sperm-lysin)
    3.8e+02    4.7   1.3    1.6e+03    2.8   0.9    2.1  1  PF01581  FMRFamide related peptide family
    4.4e+02    3.6   0.0      1e+03    2.5   0.0    1.5  1  PF02875  Mur ligase family, glutamate ligase domain
    4.7e+02    3.2   0.1    1.3e+03    1.8   0.1    1.6  1  PF01506  Hepatitis C virus non-structural 5a protein membran


Domain and alignment annotation for each model:
>> PF04055  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   76.1   0.0   4.4e-24   2.2e-20       7     157 ..      17     210 ..      16     219 .. 0.91

  Alignments for each domain:
  == domain 1    score: 76.1 bits;  conditional E-value: 4.4e-24
                 ESS--TT-TTCTT................HHHHHCHCHHHHHHHHHHHHHHTSCEEEEEEEC--SGGGSTTHHHHHHHHHHTC................ CS
                 xxxxxxxxxxxxx................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx................ RF
     PF04055   7 CnlrCsfCanpet................sregrgrsrsveeileevkelkeekgvkevtltGgepllypdfvellerlakla................ 73 
                 C++rC+fC+ + +                + +++++  +  +i+  ++ ++    + e +++Gg+  + p+ +++++ +   +                
  AAL63125.1  17 CPGRCTFCPSSADapksympdspvvlrakRNRYDPYLQTAGRIKVYIENGHTPS-KIEAVIMGGTFSALPRGYREWFVANIYKalndfphwtssadptp 114
                 ****************************99999999999999999999997555.78888888889999999999999999999999************ PP

                 ..........EEEEEEEEEEHCCSHG...HHHHHHHHHTTSSEEEEEEESSSHHCHHHHHTCCSHHHHHHHHHHHHHHCSSETEEEEEEEEE--THH CS
                 ..........xxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
     PF04055  74 ..........lpgirialetngtlpd...eeileelaelgvdrvslglesgdeekvlklmrrghtfeevlealeklreagikrvvdfivglpgetde 157
                           ++++r++  t +t+pd   +  ++ l++lgv+rv+lg++s+ ++ vl++++rgh  +ev+ea+ +l+++  k+++++++glpg   +
  AAL63125.1 115 nleaeqirneTAELRMVALTVETRPDfinKAEVDFLLKLGVTRVELGVQSIYDD-VLQKVKRGHGAAEVVEATAILKDSAYKVCYHVMPGLPGSDPD 210
                 ********998888888888888888888*************************.**************************************8754 PP

>> PF00583  Acetyltransferase (GNAT) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.8   0.0   2.1e-08   0.00011       6      83 .]     361     447 ..     358     447 .. 0.78

  Alignments for each domain:
  == domain 1    score: 24.8 bits;  conditional E-value: 2.1e-08
                 EEEEEEEEEEETTTTTC.......TTEEEEEEEEES.....GGGTTTT-HHHHHHHHHHHHHHCTCSEEEEEEETTGHHHHHHHHHTT-E CS
     PF00583   6 elvGfaslsvigedgra.......ertayieglaVs.....peyrgqGiGkaLleallekarerglerielevesgndraiklYeklGFk 83 
                 +l + ++l+++++++r        +r+++++g aV        +++ G G++L++ ++e+a e g+ +i+++ ++g +   ++Y+klG++
  AAL63125.1 361 TLYAILRLRIPNRPHRPelykaalVRELHVYGPAVPvgkqgIWWQHSGMGRELMRLAEEIAGEFGALKIAVISGVGVR---EYYRKLGYE 447
                 556666677777654223445556666666666666666666799*********************************...*******96 PP

>> PF02145  Rap/ran-GAP
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   0.0    0.0015       7.6      13      72 ..     148     213 ..     145     222 .. 0.82

  Alignments for each domain:
  == domain 1    score: 8.5 bits;  conditional E-value: 0.0015
     PF02145  13 eFlssLG.ekvkLkdhkkyrGgLdtknnttGehs.....iytkdkdveimFhVstmlpsnesdkqq 72 
                 +Fl +LG ++v+L  +++y   L++ +  +G  +        kd+ + + +hV + lp ++ d+ +
  AAL63125.1 148 DFLLKLGvTRVELGVQSIYDDVLQKVKRGHGAAEvveatAILKDSAYKVCYHVMPGLPGSDPDRDL 213
                 7999**9668******************999888222224456779************99888765 PP

>> PF03454  MoeA C-terminal region (domain IV)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   0.0    0.0041        20       2      38 ..     364     401 ..     363     413 .. 0.85

  Alignments for each domain:
  == domain 1    score: 7.9 bits;  conditional E-value: 0.0041
                 EEESS--B-----EEEEEEEE..E....EEEEE---.. CS
     PF03454   2 arlaedlksdpgrreflRvrlted.dgkyyaepigkqg 38 
                 a+l+ ++++ p+r+e +++ l ++ +  + a+p+gkqg
  AAL63125.1 364 AILRLRIPNRPHRPELYKAALVRElHVYGPAVPVGKQG 401
                 78999*****************9965558888999974 PP

>> PF07081  Protein of unknown function (DUF1349)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0   0.0    0.0044        22     117     148 ..     274     305 ..     267     323 .. 0.86

  Alignments for each domain:
  == domain 1    score: 7.0 bits;  conditional E-value: 0.0044
     PF07081 117 wlrlsrrgdalaieasldgkewkllRlahlee 148
                 w+r+ r g+++ +++ ldg +w  +R++ l++
  AAL63125.1 274 WVRVMRFGRDIPLHHVLDGPRWGNMRQIVLKH 305
                 9*************************998664 PP

>> PF04909  Amidohydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   0.0     0.019        94      21     105 ..      48     139 ..      41     146 .. 0.75

  Alignments for each domain:
  == domain 1    score: 5.1 bits;  conditional E-value: 0.019
                 CSCCCCECCHHHHHHSCHCCCCEHHHH.......HHCCHHCHHHHHHHHHHHTTTCEE--TT-TTSHHHHHHHHHHHHHC------EEECCH CS
     PF04909  21 gvdpqlasaaallvliaalgvaradev.......aasargannrlaaeaakrpdrflggaalpprdpedavaelerrveelgfkGvklhphl 105
                 ++dp+l++a    v+i+     +  e+        a+ rg+ ++++a++ k+  +f  +  +++++p  ++++++   +el+ +++ + +++
  AAL63125.1  48 RYDPYLQTAGRIKVYIENGHTPSKIEAvimggtfSALPRGYREWFVANIYKALNDFPHWTSSADPTPNLEAEQIRNETAELRMVALTVETRP 139
                 5555555555555555543333333333444444678899**************************************9*999998887765 PP

>> PF11905  Domain of unknown function (DUF3425)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0   0.0     0.013        66      13      55 ..     265     307 ..     257     340 .. 0.87

  Alignments for each domain:
  == domain 1    score: 6.0 bits;  conditional E-value: 0.013
     PF11905  13 qetyeklpeslrPtplQltipHppwiDllpwPklRdrLiraas 55 
                 +++y+++p+++r  +  + ip ++++D   w ++R+ ++++ +
  AAL63125.1 265 AKIYASIPRWVRVMRFGRDIPLHHVLDGPRWGNMRQIVLKHME 307
                 678999*****************************99888766 PP

>> PF08992  Quinohemoprotein amine dehydrogenase, gamma subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   0.1      0.84   4.2e+03      41      61 ..      91     111 ..      88     118 .. 0.88
   2 ?    3.4   0.0     0.083   4.1e+02      43      69 ..     223     249 ..     210     258 .. 0.89

  Alignments for each domain:
  == domain 1    score: 0.2 bits;  conditional E-value: 0.84
                 SSTTTS--TTTT-TTTT---- CS
     PF08992  41 wwpaqvpdtlstykdwskdad 61 
                 w+ a++   l+ +++w++ ad
  AAL63125.1  91 WFVANIYKALNDFPHWTSSAD 111
                 9999999*********99876 PP

  == domain 2    score: 3.4 bits;  conditional E-value: 0.083
                 TTTS--TTTT-TTTT----SHHHHGGG CS
     PF08992  43 paqvpdtlstykdwskdaddakedwrk 69 
                 p+ +pd ++ y+ +    ++ +edwr+
  AAL63125.1 223 PSYMPDCVKIYPLYVVPNTELSEDWRR 249
                 8899*********************95 PP

>> PF07661  MORN repeat variant
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.0   0.0      0.19   9.5e+02       3      15 ..     250     262 ..     248     267 .. 0.87

  Alignments for each domain:
  == domain 1    score: 3.0 bits;  conditional E-value: 0.19
     PF07661   3 GeekeYyenGklk 15 
                 G +k+Y+e+ +l+
  AAL63125.1 250 GLYKSYDEETWLE 262
                 99******98876 PP

>> PF08101  Domain of unknown function (DUF1708)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   0.0      0.04     2e+02      13      53 ..     183     223 ..     171     228 .. 0.87

  Alignments for each domain:
  == domain 1    score: 3.1 bits;  conditional E-value: 0.04
     PF08101  13 hliteeLKargldtpflllpfrpesddeklrtflrsifpka 53 
                   +t+ LK  + ++ + ++p  p sd++   +++r+if++ 
  AAL63125.1 183 VEATAILKDSAYKVCYHVMPGLPGSDPDRDLEMVREIFSNP 223
                 45799*********************************875 PP

>> PF06808  DctM-like transporters
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.9   0.1     0.042   2.1e+02      65      97 ..     401     432 ..     400     437 .. 0.78

  Alignments for each domain:
  == domain 1    score: 2.9 bits;  conditional E-value: 0.042
     PF06808  65 GillersGlaerlidlaaalvGrvrGGlakvsi 97 
                 Gi  ++sG++++l++la +++G++ G l  ++i
  AAL63125.1 401 GIWWQHSGMGRELMRLAEEIAGEF-GALKIAVI 432
                 67789*****************98.44444444 PP

>> PF09005  Domain of unknown function (DUF1897)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.8   0.9      0.11   5.4e+02      17      27 ..     439     449 ..     438     453 .. 0.89

  Alignments for each domain:
  == domain 1    score: 2.8 bits;  conditional E-value: 0.11
     PF09005  17 EYYrqiGdhee 27 
                 EYYr++G +++
  AAL63125.1 439 EYYRKLGYERC 449
                 9******9886 PP

>> PF08844  Domain of unknown function (DUF1815)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.3   0.0     0.081   4.1e+02      63      83 ..     397     417 ..     385     427 .. 0.89

  Alignments for each domain:
  == domain 1    score: 3.3 bits;  conditional E-value: 0.081
     PF08844  63 vsdlgiswvesrddrelvkle 83 
                 v ++gi w  s  +rel++l 
  AAL63125.1 397 VGKQGIWWQHSGMGRELMRLA 417
                 6789***************94 PP

>> PF07659  Domain of Unknown Function (DUF1599)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.5   0.0     0.098   4.9e+02      11      27 ..     159     175 ..     157     186 .. 0.91

  Alignments for each domain:
  == domain 1    score: 3.5 bits;  conditional E-value: 0.098
     PF07659  11 ilrvsSltdqiliKvnR 27 
                 +l+v+S+ d +l+Kv+R
  AAL63125.1 159 ELGVQSIYDDVLQKVKR 175
                 589*************9 PP

>> PF00880  Nebulin repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.8   0.0      0.13   6.3e+02       1      12 [.      37      48 ..      37      49 .. 0.91

  Alignments for each domain:
  == domain 1    score: 2.8 bits;  conditional E-value: 0.13
     PF00880  1 DtPeivhAKkna 12
                D+P +++AK+n 
  AAL63125.1 37 DSPVVLRAKRNR 48
                99********96 PP

>> PF12163  DNA replication regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5   0.0     0.099     5e+02      35      68 ..      70     103 ..      65     117 .. 0.91

  Alignments for each domain:
  == domain 1    score: 2.5 bits;  conditional E-value: 0.099
                 HHHHHHH----EEEEE-GGGHHHHHHHHHHHS-S CS
     PF12163  35 salkkllegksvivitDeereWfedYilkkinks 68 
                 s+++ ++ g ++  +    reWf   i k +n+ 
  AAL63125.1  70 SKIEAVIMGGTFSALPRGYREWFVANIYKALNDF 103
                 689999************************9975 PP

>> PF01303  Egg lysin (Sperm-lysin)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5   0.0      0.15   7.6e+02      80     117 ..     295     332 ..     292     340 .. 0.93

  Alignments for each domain:
  == domain 1    score: 2.5 bits;  conditional E-value: 0.15
                 HHHHHHHHHHHHHCHT---SHHHCCC--------S-HH CS
     PF01303  80 wqnYmewvskkikkLgrkpnkkdyrrlGaeiGrriple 117
                 w n+ ++v k++++Lg k  +   r++G ++++++p++
  AAL63125.1 295 WGNMRQIVLKHMERLGLKCQEIRCREVGIKLANNVPIQ 332
                 999****************************9988875 PP

>> PF01581  FMRFamide related peptide family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.8   0.9      0.33   1.6e+03       7      11 .]     278     282 ..     276     282 .. 0.89

  Alignments for each domain:
  == domain 1    score: 2.8 bits;  conditional E-value: 0.33
     PF01581   7 mRFGR 11 
                 mRFGR
  AAL63125.1 278 MRFGR 282
                 9***9 PP

>> PF02875  Mur ligase family, glutamate ligase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5   0.0       0.2     1e+03       7      31 ..      52      76 ..      48      85 .. 0.91

  Alignments for each domain:
  == domain 1    score: 2.5 bits;  conditional E-value: 0.2
                EEECETTTEEEE-T--SCCCHHHHH CS
     PF02875  7 vvgeangvtvidDyahnpdslsaal 31
                ++++a+ ++v++  +h+p  ++a++
  AAL63125.1 52 YLQTAGRIKVYIENGHTPSKIEAVI 76
                5788999***************997 PP

>> PF01506  Hepatitis C virus non-structural 5a protein membrane anchor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.8   0.1      0.26   1.3e+03      11      18 ..     277     284 ..     277     284 .. 0.91

  Alignments for each domain:
  == domain 1    score: 1.8 bits;  conditional E-value: 0.26
     PF01506  11 Vcrvlrdf 18 
                 V+r++rd+
  AAL63125.1 277 VMRFGRDI 284
                 9*****95 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (471 residues)
Target model(s):                       11912  (2158902 nodes)
Passed MSV filter:                       205  (0.0172095); expected 238.2 (0.02)
Passed bias filter:                      190  (0.0159503); expected 238.2 (0.02)
Passed Vit filter:                        21  (0.00176293); 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):              20  [number of targets reported over threshold]
# CPU time: 0.25u 0.10s 00:00:00.35 Elapsed: 00:00:01
# Mc/sec: 4067.37
//