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/F49D11.1
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Query:  F49D11.1  CE28405    status:Partially_confirmed TR:O44729 protein_id:AAB96707.2

Scores for sequence family classification (score includes all domains):
Model    Description                                    Score    E-value  N
-------- -----------                                    -----    ------- ---
WD40     WD domain, G-beta repeat                       164.0    2.5e-45   6
FliO     Flagellar biosynthesis protein, FliO             6.2        1.1   1
ku       Ku70/Ku80 beta-barrel domain                     4.7        1.4   1

Parsed for domains:
Model    Domain  seq-f seq-t    hmm-f hmm-t      score  E-value
-------- ------- ----- -----    ----- -----      -----  -------
ku         1/1     183   203 ..   215   237 .]     4.7      1.4
FliO       1/1     190   208 ..    79    99 .]     6.2      1.1
WD40       1/6     265   304 ..     1    39 []    36.6  1.3e-08
WD40       2/6     309   347 ..     1    39 []    32.5  1.9e-07
WD40       3/6     351   391 ..     1    39 []    12.2     0.11
WD40       4/6     395   433 ..     1    39 []    32.7  1.7e-07
WD40       5/6     484   524 ..     1    39 []    23.8  5.8e-05
WD40       6/6     528   567 .]     1    39 []    28.2  3.3e-06

Alignments of top-scoring domains:
ku: domain 1 of 1, from 183 to 203: score 4.7, E = 1.4
                   *->npaetdakpteeqldlakqlidk<-*
                      ++++   kpt+e + +++++++k
    F49D11.1   183    EKTVA--KPTPELQKQMDEIVKK    203

FliO: domain 1 of 1, from 190 to 208: score 6.2, E = 1.1
                   *->tPeFqqrLkeLlkKhdpkgKs<-*
                      tPe+q+++ e  kK    +Ks
    F49D11.1   190    TPELQKQMDEIVKK--RQEKS    208

WD40: domain 1 of 6, from 265 to 304: score 36.6, E = 1.3e-08
                   *->geclatl.gHtspvtcvafspdsgpylasgSrDgtiklWd<-*
                      +++++t++gH+++v+ + + p s ++++s+S D +iklW+
    F49D11.1   265    KKLVHTYrGHNKGVNFLQWFPKSAHLFLSCSMDTKIKLWE    304

WD40: domain 2 of 6, from 309 to 347: score 32.5, E = 1.9e-07
                   *->geclatl.gHtspvtcvafspdsgpylasgSrDgtiklWd<-*
                        +++t+ gH+ pv+ vaf+ + g+ ++s+S D+ +klWd
    F49D11.1   309    QRVVRTYaGHKLPVREVAFNNE-GTEFLSASFDRYVKLWD    347

WD40: domain 3 of 6, from 351 to 391: score 12.2, E = 0.11
                   *->geclatl.gHtspvtcvafspd..sgpylasgSrDgtiklWd<-*
                      g++++ ++   +  +c++++pd++  ++++ g  +++i  Wd
    F49D11.1   351    GQVKQRFhTG-HVPYCLKYHPDddKNHMFLVGMQNKKIIQWD    391

WD40: domain 4 of 6, from 395 to 433: score 32.7, E = 1.7e-07
                   *->geclatl.gHtspvtcvafspdsgpylasgSrDgtiklWd<-*
                      ge +++++ H  +v+++ f     +++as S+D+++++W+
    F49D11.1   395    GEIVQEYdRHLQAVNSITFFDK-NRRFASTSDDKSVRIWE    433

WD40: domain 5 of 6, from 484 to 524: score 23.8, E = 5.8e-05
                   *->geclatl.gHtspvtcvafspd.sgpylasgSrDgtiklWd<-*
                       + ++ ++gH+++ +++ ++ ++++++l+sg +Dg++ +Wd
    F49D11.1   484    FSKKKAFrGHNAAGYACNIDFSpDQSFLISGDADGKLFIWD    524

WD40: domain 6 of 6, from 528 to 567: score 28.2, E = 3.3e-06
                   *->geclatl.gHtspvtcvafspdsgpylasgSrDgtiklWd<-*
                       + +   ++H s++ +  ++p++ ++++++++Dg ik+W+
    F49D11.1   528    HKIVGKWkAHDSTCIAALWHPHEKSRMITAGWDGLIKMWN    567



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