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