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:            hmm3/seq/F49E7.1a
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Query:  F49E7.1a  CE26367    status:Partially_confirmed TR:Q9GYH7 protein_id:AAF98624.1

Scores for sequence family classification (score includes all domains):
Model    Description                                    Score    E-value  N
-------- -----------                                    -----    ------- ---
VPS9     Vacuolar sorting protein 9 (VPS9) domain        93.4    4.5e-24   1
RasGAP   GTPase-activator protein for Ras-like GTPase     7.5       0.81   1
ARID     ARID/BRIGHT DNA binding domain                   5.7        2.9   1
Microcin Colicin E1 (microcin) immunity protein           5.6        5.1   1
Clathrin Region in Clathrin and VPS                       5.2        4.6   1
TYA      TYA transposon protein                           2.6        5.6   1
DUF430   Protein of unknown function (DUF430)             2.0        6.5   1

Parsed for domains:
Model    Domain  seq-f seq-t    hmm-f hmm-t      score  E-value
-------- ------- ----- -----    ----- -----      -----  -------
RasGAP     1/1     315   330 ..   188   203 ..     7.5     0.81
Clathrin   1/1     362   394 ..   126   158 .]     5.2      4.6
TYA        1/1     571   606 ..   406   440 .]     2.6      5.6
DUF430     1/1     861   881 ..   339   359 .]     2.0      6.5
Microcin   1/1     863   893 ..    24    55 .]     5.6      5.1
ARID       1/1     908   928 ..     1    21 [.     5.7      2.9
VPS9       1/1    1006  1108 ..     1   116 [.    93.4  4.5e-24

Alignments of top-scoring domains:
RasGAP: domain 1 of 1, from 315 to 330: score 7.5, E = 0.81
                   *->FinPAIvsPdlfnIid<-*
                      +i+PAI+sP+ f+ +d
    F49E7.1a   315    LICPAIISPQKFGVVD    330

Clathrin: domain 1 of 1, from 362 to 394: score 5.2, E = 4.6
                   *->yqkavdyavkrnnpelwaevlkacldkkrflla<-*
                      ++ +++++++++n+ l +e++ a+l +k   ++
    F49E7.1a   362    PEEYKEFLSQCRNTHLISEMMDALLVEKLAPDV    394

TYA: domain 1 of 1, from 571 to 606: score 2.6, E = 5.6
                   *->SskfsrvdNDsIskST.vesiyLsddndLsLrqetk<-*
                      Ss +  ++  + s ST+v++  L    +L  + +
    F49E7.1a   571    SSGSAETNSEHLSDSTsVSPEPLTSTEELQIGDQGV    606

DUF430: domain 1 of 1, from 861 to 881: score 2.0, E = 6.5
                   *->LrrrLgdkelvrrriaarive<-*
                      L+rrL+++ lv  ++++ + +
    F49E7.1a   861    LNRRLTEQILVDFLMRTFLET    881

Microcin: domain 1 of 1, from 863 to 893: score 5.6, E = 5.1
                   *->kyaiEhialkfikkeFfvkrKNlnseppaKlg<-*
                      +++ E i   f  + F +++ N n+ +++K++
    F49E7.1a   863    RRLTEQILVDFLMRTFLETGFN-NKHTVGKTQ    893

ARID: domain 1 of 1, from 908 to 928: score 5.7, E = 2.9
                   *->eaqtrerkeFldrLikFmekr<-*
                      ++ + er+eFl+ L+ F+++r
    F49E7.1a   908    LRAQDERAEFLKNLLTFLRDR    928

VPS9: domain 1 of 1, from 1006 to 1108: score 93.4, E = 4.5e-24
                   *->fleeakqeLrelqYeyysPrdKlqcllkvcklifnalkltkgenaaP
                      ++++a+ eL  l+  y + +dKl+c+ ++c +i n+  l ++   a
    F49E7.1a  1006    PWPSAQAELSMLD-IYVTAQDKLNCVVRCCDVINNLVALSSKN--A- 1048

                   DPmCYRqlsADdFLPvLiYvvlkanpphLlsnveYisrFlnpPisRlLsG
                         ++sADd+ PvL++v++kanp+ Llsnv++++ F++   +R  sG
    F49E7.1a  1049 ------VASADDLTPVLVFVIIKANPRALLSNVQFVETFAG---DRIESG 1089

                   EagYYLTsLeaAleFiktl<-*
                    ++YY+ ++++A+e ikt+
    F49E7.1a  1090 RDAYYWVNFKSAVEYIKTI    1108



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