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/C06G4.1
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Query: C06G4.1 CE28203 possible RNA binding protein status:Partially_confirmed SW:P34307 protein_id:AAA27939.2
Scores for sequence family classification (score includes all domains):
Model Description Score E-value N
-------- ----------- ----- ------- ---
KH KH domain 56.4 1.1e-14 2
RNA_pol_L RNA polymerases L / 13 to 16 kDa subunit 7.4 0.56 1
Sedlin_N Sedlin, N-terminal conserved region 4.4 5.5 1
Parsed for domains:
Model Domain seq-f seq-t hmm-f hmm-t score E-value
-------- ------- ----- ----- ----- ----- ----- -------
RNA_pol_L 1/1 639 656 .. 86 103 .] 7.4 0.56
KH 1/2 702 749 .. 1 49 [] 26.7 4.4e-06
Sedlin_N 1/1 741 753 .. 1 13 [. 4.4 5.5
KH 2/2 779 826 .. 1 49 [] 29.7 5.7e-07
Alignments of top-scoring domains:
RNA_pol_L: domain 1 of 1, from 639 to 656: score 7.4, E = 0.56
*->ledlinlcdlledkFkek<-*
+++++++c+ +++k +e
C06G4.1 639 CRSIEKYCGIIIEKMREV 656
KH: domain 1 of 2, from 702 to 749: score 26.7, E = 4.4e-06
*->evlvpasrvGliIGkgGsnIkeireetgakIdipddsegsverivti
e p s+ + iIG+ G+n+k i++ t + I ++++ +++e +++i
C06G4.1 702 EHCTPISFYRKIIGRCGENLKTIEKVTRTAIVFKRSF-DNNEACFSI 747
tg<-*
+g
C06G4.1 748 RG 749
Sedlin_N: domain 1 of 1, from 741 to 753: score 4.4, E = 5.5
*->kefyFvIVGhnDi<-*
+e++F I G+ D+
C06G4.1 741 NEACFSIRGRTDN 753
KH: domain 2 of 2, from 779 to 826: score 29.7, E = 5.7e-07
*->evlvpasrvGliIGkgGsnIkeireetgakIdipddsegsverivti
+v vp+++v+++IG++G I++ir+e++ak+ + g+ ++++++
C06G4.1 779 QVRVPENMVARLIGRHGVEINRIRSESKAKCYLNAIR-GNLDDKFMV 824
tg<-*
C06G4.1 825 CS 826