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/C33D9.1b
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Query:  C33D9.1b  CE30499  locus:exc-5 PH (pleckstrin  homology) domain status:Confirmed TR:Q968Z5 protein_id:CAD30432.1

Scores for sequence family classification (score includes all domains):
Model    Description                                    Score    E-value  N
-------- -----------                                    -----    ------- ---
RhoGEF   RhoGEF domain                                  129.6      1e-36   1
PH       PH domain                                       81.0      2e-21   2

Parsed for domains:
Model    Domain  seq-f seq-t    hmm-f hmm-t      score  E-value
-------- ------- ----- -----    ----- -----      -----  -------
RhoGEF     1/1     301   479 ..     1   207 []   129.6    1e-36
PH         1/2     510   613 ..     1    85 []    62.3  3.7e-16
PH         2/2     720   811 ..     1    85 []    18.6  0.00076

Alignments of top-scoring domains:
RhoGEF: domain 1 of 1, from 301 to 479: score 129.6, E = 1e-36
                   *->vlkElleTEkkYvrdLeildnvymkpLreaaisskpvltpddietiF
                      ++kEl+ +E  Yv+ L +l ++++ +L +++     ++t d+i  +
    C33D9.1b   301    AAKELVDSEQRYVDKLKLLGDTFRNRLIKEE-----LITNDKITRLL 342

                   sNiediyefhreFLkssLearisssqfedlDekkiepsaqrlGdlFlklk
                   +N+ ++y+fh++ +++ L + i+++             + r++ ++ k
    C33D9.1b   343 ANVSSLYQFHNTHFLPQLLESIRDW-----------HTTKRIANVVRKQ- 380

                   epflqvYgeYcsnkpyAqelleklrqaasnpqFaefldeveassntgAkd
                   +pfl++Y eY +n+++A +l e l+   +  +Fa +++e+e+ + ++
    C33D9.1b   381 APFLKMYSEYTNNYDRATKLFEELK---KKKKFADVVKEIEKQAECE--- 424

                   davkltLqsLLlkPvqRilrYpLLLkeLLkhtpegedqpdredLkkaldl
                       l L ++L+ PvqR+ rY+LLL+e++kh ++  ++ d  d   al+l
    C33D9.1b   425 ---GLPLGHHLICPVQRVMRYQLLLQEYKKHLQP--SDVDFDDTTVALEL 469

                   lqdlaksiNe<-*
                   +  +a + Ne
    C33D9.1b   470 VLQAAAHANE    479

PH: domain 1 of 2, from 510 to 613: score 62.3, E = 3.7e-16
                   *->vikeGwLlkks...kswkkRyfvLfndvLlyykdsk......kkpkg
                      + k+G ++k s+++++ ++R+++Lfnd  ++  ++k  + +++k++
    C33D9.1b   510    LLKSGSVQKISsttEKTEERFIFLFNDLVILASERKmigvskYKLRA 556

                   sipLsgcqvek.pd...kncFeirt.dr.....tlllqaeseeerkeWvk
                   +++ s++qv+++++ +++++F++r +d+++++++++l++++++e+++Wv+
    C33D9.1b   557 VFSASHMQVCEgDNlerEHSFYLRGsDGtgpkrCVELFTPTQKEKNDWVD 606

                   aiqsair<-*
                   +i s+i
    C33D9.1b   607 SIFSIID    613

PH: domain 2 of 2, from 720 to 811: score 18.6, E = 0.00076
                   *->vikeGwLlkks..kswkkRyfvLfn.dvLlyykdsk.kkpkgsipLs
                      v ++  ++ +++ ++  +R++v++++ +++ y ++ +     ++pL
    C33D9.1b   720    VLHSSQIRFRGslGKLLDRFMVVRDdFCMYTYSSEEdICALAMLPLP 766

                   gcqvek.pdkncFeirt.dr.tlllqaeseeerkeWvkaiqsair<-*
                   gc+v+   +k++F +r + r+ + + ae+e+   +W++ +  a++
    C33D9.1b   767 GCEVKMcGEKFTFSVRVgARrMYTMTAEDEQTQMKWLAILDLAAN    811



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