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/C35B8.1
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Query: C35B8.1 CE02534 Cuticle collagen status:Partially_confirmed TR:Q18480 protein_id:AAC46553.1
Scores for sequence family classification (score includes all domains):
Model Description Score E-value N
-------- ----------- ----- ------- ---
Collagen Collagen triple helix repeat (20 copies 93.3 3.7e-24 3
Col_cuticle_N Nematode cuticle collagen N-terminal do 68.1 7.5e-19 1
Parsed for domains:
Model Domain seq-f seq-t hmm-f hmm-t score E-value
-------- ------- ----- ----- ----- ----- ----- -------
Col_cuticle_N 1/1 12 73 .. 1 66 [] 68.1 7.5e-19
Collagen 1/3 100 131 .. 29 60 .] 23.5 5.8e-05
Collagen 2/3 148 207 .. 1 60 [] 37.4 8.4e-09
Collagen 3/3 217 276 .. 1 60 [] 47.8 1.2e-11
Alignments of top-scoring domains:
Col_cuticle_N: domain 1 of 1, from 12 to 73: score 68.1, E = 7.5e-19
*->SgvAvlacLftvpsiyndInsfqdevmdemdeFKvyaddaWneMvdv
S+v++ a+L++v++i+ndIn + +++ +m++FK+++d aW ++++
C35B8.1 12 SAVVITASLCSVLVIMNDINKLSEDISIGMENFKDVSDVAWGNIMVL 58
qrnvrppskpasarfgrpf<-*
+ +vr++ sa r+
C35B8.1 59 HGGVRQQ----SASVHRDV 73
Collagen: domain 1 of 3, from 100 to 131: score 23.5, E = 5.8e-05
*->ppGppGepGpPGppGppGppGppGapGapGpp<-*
p+G pGe+G+PG +G pGp G++G++GapG +
C35B8.1 100 PAGSPGEKGEPGLAGLPGPDGEDGKDGAPGVA 131
Collagen: domain 2 of 3, from 148 to 207: score 37.4, E = 8.4e-09
*->GppGppGppGppGppGppGppGpaGapGppGppGepGpPGppGppGp
Gp+Gp+G +GppGppG+ G pG++G pG++G pG+ G+PG G pGp
C35B8.1 148 GPRGPRGDAGPPGPPGNGGRPGQRGTPGEAGTPGPVGEPGETGGPGP 194
pGppGapGapGpp<-*
+G pG+ G+pG+p
C35B8.1 195 QGRPGQRGEPGQP 207
Collagen: domain 3 of 3, from 217 to 276: score 47.8, E = 1.2e-11
*->GppGppGppGppGppGppGppGpaGapGppGppGepGpPGppGppGp
G+pGp+Gp+G +G+pG+ G +G++G G +G+pG +G+ G+ G++G+
C35B8.1 217 GRPGPQGPRGQQGEPGKDGSKGNPGDEGRQGHPGKNGRTGAHGKDGA 263
pGppGapGapGpp<-*
pG G+ G+ Gp
C35B8.1 264 PGKCGKEGPIGPD 276