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/B0303.4
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Query: B0303.4 CE29540 status:Partially_confirmed SW:P34256 protein_id:AAA27898.3
Scores for sequence family classification (score includes all domains):
Model Description Score E-value N
-------- ----------- ----- ------- ---
ubiquitin Ubiquitin family 53.5 1.7e-13 1
MTD methylene-5,6,7,8-tetrahydromethanopteri 4.0 3.6 1
Thioesterase Thioesterase domain 2.9 7.3 1
Parsed for domains:
Model Domain seq-f seq-t hmm-f hmm-t score E-value
-------- ------- ----- ----- ----- ----- ----- -------
MTD 1/1 340 354 .. 267 281 .] 4.0 3.6
Thioesterase 1/1 357 388 .. 231 267 .] 2.9 7.3
ubiquitin 1/1 341 415 .. 1 83 [] 53.5 1.7e-13
Alignments of top-scoring domains:
MTD: domain 1 of 1, from 340 to 354: score 4.0, E = 3.6
*->dGKvLsKkkLmekPE<-*
+GK+L K k+m + E
B0303.4 340 EGKILIKLKFMNDTE 354
Thioesterase: domain 1 of 1, from 357 to 388: score 2.9, E = 7.3
*->eytpgafdvrmlpGdHFylledhveleevlehilral<-*
+y +++ +v ++ +dHF+ l ++ +v++ i +
B0303.4 357 TYASLEDTVAKFKVDHFTNL-AN----QVIRLIYQGQ 388
ubiquitin: domain 1 of 1, from 341 to 415: score 53.5, E = 1.7e-13
*->mkifVKtldgkgkvtdgstitlevepsdTVlelKekIedkegippeq
ki +K + + + +s K k+ + ++++ +
B0303.4 341 GKILIKLKFMN-------DTEKNTYASLEDTVAKFKVDHFTNLANQV 380
QrLiyaGkvLreDdttLaeYniqegsftlhlvlrlr<-*
+rLiy+G+ LreD++tL+eY++q+gs ++h +++++
B0303.4 381 IRLIYQGQLLREDHRTLEEYGLQPGS-IVHCHISTT 415