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: hmm5/seq/Y43B11AR.4
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Query: Y43B11AR.4 CE24278 status:Confirmed TR:Q9N3X2 protein_id:AAF60569.1
Scores for sequence family classification (score includes all domains):
Model Description Score E-value N
-------- ----------- ----- ------- ---
Ribosomal_S4e Ribosomal family S4e 113.9 1.3e-31 1
KOW KOW motif 24.5 8.7e-05 1
S4 S4 domain 6.6 6.5 1
Parsed for domains:
Model Domain seq-f seq-t hmm-f hmm-t score E-value
-------- ------- ----- ----- ----- ----- ----- -------
S4 1/1 41 89 .. 1 48 [] 6.6 6.5
Ribosomal_S4e 1/1 93 169 .. 1 85 [] 113.9 1.3e-31
KOW 1/1 174 210 .. 1 40 [] 24.5 8.7e-05
Alignments of top-scoring domains:
S4: domain 1 of 1, from 41 to 89: score 6.6, E = 6.5
*->mRLDkvL.arlglasSrseArqlIrhGhVrVNGkvvkdpsyrvkpgD
L +L+ rl++a +eA+++ ++ VrV+Gkv + +++ +D
Y43B11AR.4 41 LPLSLFLrNRLKYALNYTEAKKILTQRVVRVDGKVRTCHKFPTGFMD 87
ei<-*
++
Y43B11AR.4 88 VV 89
Ribosomal_S4e: domain 1 of 1, from 93 to 169: score 113.9, E = 1.3e-31
*->ktnenYRvlyDekGRlvlheIsdEdAkyKLcKvrnktlgkgGvpqLn
+tne++R lyD+kGR+v+h+I + +A++KLcKv+++ ++ +Gvp L
Y43B11AR.4 93 RTNEYFRMLYDTKGRYVVHRIQAAEADFKLCKVKSVRTVNKGVPVLT 139
lhDGRtliikyddpsKAEedlikvgDsikislpeqeIv<-*
+ DGRt i+y+dp kv+D+i+ + +q+I+
Y43B11AR.4 140 TTDGRT--IRYPDP------HVKVNDTIVFNISTQKIT 169
KOW: domain 1 of 1, from 174 to 210: score 24.5, E = 8.7e-05
*->fkkGdvVrVisGpfkGkkGkVvevdpkkGHGslknrVvve<-*
f++G++++V++G++ G++G++ ++++ G ++ +++++
Y43B11AR.4 174 FEPGNLAYVTGGRNVGRVGIIGHRERLP--GASD-IIHIK 210