Motif confirmation by HMMer


hmmpfam - search a single seq against HMM database
HMMER 2.1.1 (Dec 1998)
Copyright (C) 1992-1998 Washington University School of Medicine
HMMER is freely distributed under the GNU General Public License (GPL).
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HMM file:                 /home/niguts/usr02/tshini/ykclst/db/Pfam_fs
Sequence file:            hmm2/seq/F10B5.7
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Query:  F10B5.7  CE02178  locus:rrf-3  status:Partially_confirmed TR:Q19285 protein_id:CAA91312.1

Scores for sequence family classification (score includes all domains):
Model         Description                               Score    E-value  N
--------      -----------                               -----    ------- ---
RdRP          RNA dependent RNA polymerase              751.7   1.8e-230   1
ACBP          Acyl CoA binding protein                    5.4        3.9   1
EAV_env_prot  Equine arteritis virus small envelope g     4.3        1.3   1
CD36          CD36 family                                 3.4        4.7   1
UvrD-helicase UvrD/REP helicase                           2.3        8.3   1
Hemagglutinin Hemagglutinin                               0.7        3.6   1

Parsed for domains:
Model         Domain  seq-f seq-t    hmm-f hmm-t      score  E-value
--------      ------- ----- -----    ----- -----      -----  -------
EAV_env_prot    1/1      40    48 ..   214   222 .]     4.3      1.3
Hemagglutinin   1/1     312   322 ..   309   319 ..     0.7      3.6
CD36            1/1     418   441 ..   544   567 .]     3.4      4.7
RdRP            1/1     851  1243 ..     1   450 []   751.7 1.8e-230
ACBP            1/1    1329  1344 ..    74    89 .]     5.4      3.9
UvrD-helicase   1/1    1452  1503 ..   601   664 .]     2.3      8.3

Alignments of top-scoring domains:
EAV_env_prot: domain 1 of 1, from 40 to 48: score 4.3, E = 1.3
                   *->ssGtLPrRK<-*
                      ssGtLP RK
     F10B5.7    40    SSGTLPNRK    48

Hemagglutinin: domain 1 of 1, from 312 to 322: score 0.7, E = 3.6
                   *->NvskiaiGeCP<-*
                      N+s+iaiG+CP
     F10B5.7   312    NISAIAIGNCP    322

CD36: domain 1 of 1, from 418 to 441: score 3.4, E = 4.7
                   *->mkdetvntlwlqlvlvprivgviq<-*
                      m+ et+n++++q+ ++p + ++i+
     F10B5.7   418    MSHETTNSIYIQMKNPPHLWEGIP    441

RdRP: domain 1 of 1, from 851 to 1243: score 751.7, E = 1.8e-230
                   *->eipDiegkpcIhsdGtgYcFsDGvGmiSlnklArkvarklnldrgGs
                      ++pDieg+     ++++YcFsDG+G+iS+ klA++++++l+l
     F10B5.7   851    VEPDIEGG-----VENKYCFSDGCGRISI-KLATHISKILQL----- 886

                   rvkevPsAfQiRygydGyAyKGVlavdpnlddirnWkgrkvqlRpSMiKF
                     kevP++fQ+R++  G  +KG+l++dp++ddi+n  ++kv++R+S++KF
     F10B5.7   887 --KEVPACFQVRFK--G--FKGILVIDPTIDDIIN--MPKVIFRKSQQKF 928

                   eadskntlleqlEvvkfsrpspvtLNRqlItlLsqlGVedsvfeemRiTn
                    +++ + ++e+lEvvk+++pspv+LNR++It+L+q+++++s+++++RiTn
     F10B5.7   929 GEGGGELQDEYLEVVKYAMPSPVCLNRPFITILDQVSEKQSASSHRRITN 978

                   qeellldlnalleskqkaqevlaanklgenyrltidilalmliaGfelsd
                   + +++l+++ ++ s++ ++e++aa++l ++++l+id++a++++aGfels
     F10B5.7   979 RVHYYLERELCSLSNMLINENQAAEELVNRTNLAIDWNAASKRAGFELSV 1028

                   EPflrsmLsllrksklreLkeKarIfvPideGrsLlGvvDEtGtLehygq
                   +P +r+mL+++++++++++++Ka+If+P+++Grs++GvvDEtG L+ ygq
     F10B5.7  1029 DPLIRDMLFSIYRYNIIHHISKAKIFLPPSLGRSMYGVVDETGLLQ-YGQ 1077

                   VfvqvskldiekllpktsnrkksgksklevitGtVlVtKNPcLHPGDVRV
                   Vf+q+s++++     +tsnr     +  +++tG+Vl+tKNPc++PGDVRV
     F10B5.7  1078 VFIQYSPSIR-----QTSNR-----P--ILKTGKVLITKNPCHVPGDVRV 1115

                   lkAVdvPaLehyvGNlkdvVvFPQkGpRphpdecSGsDLDGDeYFVIWDq
                   ++AV++PaL+h    l+dvVvFPQ+GpRphpde++GsDLDGDeY++IWDq
     F10B5.7  1116 FDAVWQPALAH----LVDVVVFPQHGPRPHPDEMAGSDLDGDEYSIIWDQ 1161

                   kLlpernpeePmlsesekskiyiGrepseldreetdeeliefFvstkYlk
                   ++l+++n ee+m+++s++        ++e+d+e+t+++++efF++  Yl+
     F10B5.7  1162 EMLLDYN-EEAMVFPSSS--------AAEEDKEPTTDDMVEFFLR--YLQ 1200

                   sdslGlIsnAHlaiaDrfltLGDerepekarskkCleLAklhsdAVDfpK
                   +ds+G++s+AHla+aD         ++++++  +C+++A ++++AVDfpK
     F10B5.7  1201 QDSIGRMSHAHLAYAD--------LHGLFHE--NCHAIALKCAVAVDFPK 1240

                   tGv<-*
                   +Gv
     F10B5.7  1241 SGV    1243

ACBP: domain 1 of 1, from 1329 to 1344: score 5.4, E = 3.9
                   *->mkaYIakVeeLiakya<-*
                      + +Y++ + +L+++y+
     F10B5.7  1329    RDEYVDRMQQLLDEYG    1344

UvrD-helicase: domain 1 of 1, from 1452 to 1503: score 2.3, E = 8.3
                   *->efqalkqleeklgiakllkalsaraykklkdflalieelrklllsia
                      +++al++l +        ++++ ++   l   + ++   ++l+++i
     F10B5.7  1452    AWDALCDLRR--------QLMLDKNDAVL---RGKYPIAARLEEEI- 1486

                   elslealldevlellgy<-*
                   e+s+e ++d++l+l ++
     F10B5.7  1487 ENSIERQFDKFLKLKDL    1503



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