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:            hmm1/seq/C35D10.4
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Query:  C35D10.4  CE01198    status:Partially_confirmed SW:Q18486 protein_id:AAA62560.1

Scores for sequence family classification (score includes all domains):
Model    Description                                    Score    E-value  N
-------- -----------                                    -----    ------- ---
ABC1     ABC1 family                                    203.8    5.9e-60   1
SNF5     SNF5 / SMARCB1 / INI1                            2.4         10   1

Parsed for domains:
Model    Domain  seq-f seq-t    hmm-f hmm-t      score  E-value
-------- ------- ----- -----    ----- -----      -----  -------
SNF5       1/1     480   490 ..   312   322 .]     2.4       10
ABC1       1/1     395   511 ..     1   124 []   203.8  5.9e-60

Alignments of top-scoring domains:
SNF5: domain 1 of 1, from 480 to 490: score 2.4, E = 10
                   *->kkerdkdRntR<-*
                      k+e d++R++R
    C35D10.4   480    KQECDYEREAR    490

ABC1: domain 1 of 1, from 395 to 511: score 203.8, E = 5.9e-60
                   *->eeLGapieeiFaeFdeePiAaASIAQVHrAvLkdsyGeeVAVKVQrP
                       ++G+ ++e+F++Fd++P+A+ASI+QVH+AvLkd  G+ VAVKVQ+P
    C35D10.4   395    DAFGDDWREKFEHFDDKPFACASIGQVHKAVLKD--GRNVAVKVQYP 439

                   gvkkrirrDlkllkflakilkkfppggrRlrldldwivdEfrksLpqELD
                   gv++ i++D+++l  ++ +   fp+g     ++ld+ v ++r++L+qE+D
    C35D10.4   440 GVAEGIDSDIDNLVSVLSVGGIFPKG-----MFLDAFVGVARRELKQECD 484

                   flrEAanaerfrenfaddpwvyVPkVy<-*
                   ++rEA+++++fre++ad+++vyVP+V+
    C35D10.4   485 YEREARAMKKFRELIADWQDVYVPEVI    511



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