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/F55B12.3a
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Query:  F55B12.3a  CE25007  locus:sel-10 Candida CDC4 protein like status:Confirmed TN:CAB02129 protein_id:CAB02129.2

Scores for sequence family classification (score includes all domains):
Model    Description                                    Score    E-value  N
-------- -----------                                    -----    ------- ---
WD40     WD domain, G-beta repeat                       235.2    9.4e-67   7
F-box    F-box domain                                    31.2    1.4e-06   1

Parsed for domains:
Model    Domain  seq-f seq-t    hmm-f hmm-t      score  E-value
-------- ------- ----- -----    ----- -----      -----  -------
F-box      1/1     122   169 ..     1    46 []    31.2  1.4e-06
WD40       1/7     245   282 ..     1    39 []    24.2  4.4e-05
WD40       2/7     286   324 ..     1    39 []    44.0    1e-10
WD40       3/7     328   364 ..     1    39 []    47.8  8.3e-12
WD40       4/7     368   404 ..     1    39 []    39.0  2.8e-09
WD40       5/7     408   446 ..     1    39 []    38.6  3.6e-09
WD40       6/7     453   489 ..     1    39 []    22.4  0.00015
WD40       7/7     493   530 ..     1    39 []    45.0  5.5e-11

Alignments of top-scoring domains:
F-box: domain 1 of 1, from 122 to 169: score 31.2, E = 1.4e-06
                   *->fslldLPdellleIlsrLdpkdllrlslVSkrwrslvdsl.lwf.kl
                      + l++LP el ++Il +L   dll++++VSk+w+ ++  +++w++
   F55B12.3a   122    DFLSCLPVELGMKILHNLTGYDLLKVAQVSKNWKLISEIDkIWKsLG 168

                   l<-*

   F55B12.3a   169 V    169

WD40: domain 1 of 7, from 245 to 282: score 24.2, E = 4.4e-05
                   *->geclatl.gHtspvtcvafspdsgpylasgSrDgtiklWd<-*
                          a+l+gH++ v  +   +d   +l++gS+D+t+k+W
   F55B12.3a   245    IMGSAVLrGHEDHVITCMQIHD--DVLVTGSDDNTLKVWC    282

WD40: domain 2 of 7, from 286 to 324: score 44.0, E = 1e-10
                   *->geclatl.gHtspvtcvafspdsgpylasgSrDgtiklWd<-*
                      ge+ +tl gHt++v+   +s+  g+y++sgS D+t+k+W+
   F55B12.3a   286    GEVMYTLvGHTGGVWTSQISQC-GRYIVSGSTDRTVKVWS    324

WD40: domain 3 of 7, from 328 to 364: score 47.8, E = 8.3e-12
                   *->geclatl.gHtspvtcvafspdsgpylasgSrDgtiklWd<-*
                      g++l+tl+gHts+v+c+a + +   +l++gSrD t+++Wd
   F55B12.3a   328    GSLLHTLqGHTSTVRCMAMAGS---ILVTGSRDTTLRVWD    364

WD40: domain 4 of 7, from 368 to 404: score 39.0, E = 2.8e-09
                   *->geclatl.gHtspvtcvafspdsgpylasgSrDgtiklWd<-*
                      g  latl+gH ++v+cv f+     +++sg+ D t+k+W+
   F55B12.3a   368    GRHLATLhGHHAAVRCVQFDGT---TVVSGGYDFTVKIWN    404

WD40: domain 5 of 7, from 408 to 446: score 38.6, E = 3.6e-09
                   *->geclatl.gHtspvtcvafspdsgpylasgSrDgtiklWd<-*
                      g c++tl+gH++ v+++ f  + +++++sgS D +i++Wd
   F55B12.3a   408    GRCIRTLtGHNNRVYSLLFESE-RSIVCSGSLDTSIRVWD    446

WD40: domain 6 of 7, from 453 to 489: score 22.4, E = 0.00015
                   *->geclatl.gHtspvtcvafspdsgpylasgSrDgtiklWd<-*
                       ec+a l+gHts  + +    +   +l+s+ +D  +++Wd
   F55B12.3a   453    QECVALLqGHTSLTSGMQLRGN---ILVSCNADSHVRVWD    489

WD40: domain 7 of 7, from 493 to 530: score 45.0, E = 5.5e-11
                   *->geclatl.gHtspvtcvafspdsgpylasgSrDgtiklWd<-*
                      g+c++ l+gH s++t++ +     +++a++S+Dgt+klWd
   F55B12.3a   493    GTCVHMLsGHRSAITSLQWFGR--NMVATSSDDGTVKLWD    530



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