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



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