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/C34B4.1
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Query:  C34B4.1  CE08563  locus:max-1 PH (pleckstrin  homology) domain status:Partially_confirmed TR:Q18420 protein_id:CAB01487.1

Scores for sequence family classification (score includes all domains):
Model         Description                               Score    E-value  N
--------      -----------                               -----    ------- ---
PH            PH domain                                 102.5    1.7e-27   2
MyTH4         MyTH4 domain                               19.4    0.00048   2
RNA_pol_A_bac RNA polymerase Rpb3/RpoA insert domain      4.3        6.3   1

Parsed for domains:
Model         Domain  seq-f seq-t    hmm-f hmm-t      score  E-value
--------      ------- ----- -----    ----- -----      -----  -------
RNA_pol_A_bac   1/1      99   115 ..     1    18 [.     4.3      6.3
PH              1/2     249   346 ..     1    85 []    69.0  4.7e-18
PH              2/2     362   476 ..     1    85 []    33.7  4.4e-08
MyTH4           1/2     568   590 ..     1    23 [.    10.1     0.19
MyTH4           2/2     597   626 ..    89   118 .]     9.3     0.31

Alignments of top-scoring domains:
RNA_pol_A_bac: domain 1 of 1, from 99 to 115: score 4.3, E = 6.3
                   *->VyIyengSvlqDEvvaHE<-*
                      V I +++ v++ E+v H+
     C34B4.1    99    VAI-KDDKVVYSEIVKHR    115

PH: domain 1 of 2, from 249 to 346: score 69.0, E = 4.7e-18
                   *->vikeGwLlkks....kswkkRyfvLfndvLlyykdsk...kkpkgsi
                       +k+G+ +++++++ ks k+Ry+v++n+++++y++ ++++++p  +i
     C34B4.1   249    MEKSGYWTQLTdsriKSLKRRYVVFKNGQISFYRKHNnrdEEPASKI 295

                   pLsgc.qvek.pd...kncFeirt.drtlllqaeseeerkeWvkaiqsai
                   ++s++++v+k + ++  + F+++t++    +++ese+  ++Wv+ +++ai
     C34B4.1   296 SISDIrSVTKlEQqgaAYAFQLITsTDKMNFMTESERTTHDWVTILSAAI 345

                   r<-*
                   +
     C34B4.1   346 K    346

PH: domain 2 of 2, from 362 to 476: score 33.7, E = 4.4e-08
                   *->vikeGwLlkks.kswkkRyfvLfndvLlyykdsk.kkpkgsipLsgc
                        ++GwL++ + +  kk+++ L n  L+++k+s++  p g + L+g+
     C34B4.1   362    ASISGWLTRVKcGLSKKVFAALVNQKLMFFKNSNdLVPNGFLCLQGA 408

                   qvek.pd.........................kncFeirt.dr.tlllqa
                   q+ ++++++++ +++++++ +++++++++++++ ++++   + + ++l
     C34B4.1   409 QISEkHNgteeysgssdeqlettkehpnqrknNDSLCVQIaNEdPVYLIL 458

                   eseeerkeWvkaiqsair<-*
                    ++e++++W+  ++sa+
     C34B4.1   459 RTSEDKEKWLYYLKSASG    476

MyTH4: domain 1 of 2, from 568 to 590: score 10.1, E = 0.19
                   *->rsridlvqkIlkqgikrpeLRDE<-*
                      ++ idl+q Il+++  ++ LR+E
     C34B4.1   568    QYHIDLAQNILSTAVQQEYLRNE    590

MyTH4: domain 2 of 2, from 597 to 626: score 9.3, E = 0.31
                   *->aadcqerLkktqknGsRkypPsrlEieAik<-*
                      a++c+ +L +  + G+R  +PsrlE+ + +
     C34B4.1   597    AIFCESALDRCLRVGGRQEGPSRLEVTSVL    626



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