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/Y49F6B.10
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Query: Y49F6B.10 CE25334 status:Partially_confirmed TR:Q9N4U2 protein_id:AAF60736.1
Scores for sequence family classification (score includes all domains):
Model Description Score E-value N
-------- ----------- ----- ------- ---
Collagen Collagen triple helix repeat (20 copies 98.8 1.1e-25 3
Col_cuticle_N Nematode cuticle collagen N-terminal do 19.1 0.00029 1
Parsed for domains:
Model Domain seq-f seq-t hmm-f hmm-t score E-value
-------- ------- ----- ----- ----- ----- ----- -------
Col_cuticle_N 1/1 45 82 .. 1 38 [. 19.1 0.00029
Collagen 1/3 174 207 .. 27 60 .] 16.9 0.0038
Collagen 2/3 223 282 .. 1 60 [] 47.6 1.3e-11
Collagen 3/3 288 347 .. 1 60 [] 50.3 2.4e-12
Alignments of top-scoring domains:
Col_cuticle_N: domain 1 of 1, from 45 to 82: score 19.1, E = 0.00029
*->SgvAvlacLftvpsiyndInsfqdevmdemdeFKvyad<-*
S+v+v++ ++t+p+++++++s ++ em + v+a+
Y49F6B.10 45 STVSVICFCVTMPVVFTYVQSVKRQMSHEMATCNVNAR 82
Collagen: domain 1 of 3, from 174 to 207: score 16.9, E = 0.0038
*->pGppGppGepGpPGppGppGppGppGapGapGpp<-*
pGppGppG+pG+PGp G++G+ G G+pG p ++
Y49F6B.10 174 PGPPGPPGPPGRPGPNGKAGANGLNGNPGRPPEA 207
Collagen: domain 2 of 3, from 223 to 282: score 47.6, E = 1.3e-11
*->GppGppGppGppGppGppGppGpaGapGppGppGepGpPGppGppGp
Gp+G pG +G pG++G pG +G++G++G+ G++Ge+G+PGp G+ G
Y49F6B.10 223 GPKGAPGQAGYPGADGQPGSQGDNGEKGSDGAAGEKGRPGPLGKIGE 269
pGppGapGapGpp<-*
pG +G+ G+ ++
Y49F6B.10 270 PGATGETGENAEN 282
Collagen: domain 3 of 3, from 288 to 347: score 50.3, E = 2.4e-12
*->GppGppGppGppGppGppGppGpaGapGppGppGepGpPGppGppGp
Gp GppG+ Gp G +G pG+pG++G++G pG+pGe+G +G G++G
Y49F6B.10 288 GPQGPPGAIGPVGSRGTPGHPGEDGEAGAPGAPGENGTDGENGEDGV 334
pGppGapGapGpp<-*
pG pG +G +G +
Y49F6B.10 335 PGVPGHDGKAGRA 347