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: hmm4/seq/T10E10.1
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Query: T10E10.1 CE23970 collagen status:Partially_confirmed TR:Q22380 protein_id:AAA80357.2
Scores for sequence family classification (score includes all domains):
Model Description Score E-value N
-------- ----------- ----- ------- ---
Collagen Collagen triple helix repeat (20 copies 95.0 1.2e-24 4
Col_cuticle_N Nematode cuticle collagen N-terminal do 56.6 2.1e-15 1
Parsed for domains:
Model Domain seq-f seq-t hmm-f hmm-t score E-value
-------- ------- ----- ----- ----- ----- ----- -------
Col_cuticle_N 1/1 25 88 .. 1 66 [] 56.6 2.1e-15
Collagen 1/4 113 150 .. 23 60 .] 16.9 0.0036
Collagen 2/4 160 219 .. 1 60 [] 56.3 5.6e-14
Collagen 3/4 223 229 .. 54 60 .] -3.8 1.8e+03
Collagen 4/4 230 289 .. 1 60 [] 49.4 4.2e-12
Alignments of top-scoring domains:
Col_cuticle_N: domain 1 of 1, from 25 to 88: score 56.6, E = 2.1e-15
*->SgvAvlacLftvpsiyndInsfqdevmdemdeFKvyaddaWneMvdv
S A l+c++++p++yn+++++q+ ++ e+d+++ ++ ++W+e++ +
T10E10.1 25 SFTATLVCVIAAPMLYNYMQHMQSVMQSEVDFCRSRSGNIWREVTRT 71
qrnvrppskpasarfgrpf<-*
q+ + + + r +r+
T10E10.1 72 QVLAKVS--GGALRSRRQA 88
Collagen: domain 1 of 4, from 113 to 150: score 16.9, E = 0.0036
*->paGapGppGppGepGpPGppGppGppGppGapGapGpp<-*
+aG+pG pG Ge+G++G+pG+pG Gp+G++ p p+
T10E10.1 113 AAGPPGAPGQDGEDGADGQPGAPGNDGPDGPAATPAPA 150
Collagen: domain 2 of 4, from 160 to 219: score 56.3, E = 5.6e-14
*->GppGppGppGppGppGppGppGpaGapGppGppGepGpPGppGppGp
GppGp+Gp+Gp Gp G++G G++GapG++G++G pG+PG++G++G
T10E10.1 160 GPPGPAGPAGPKGPNGNSGSDGQPGAPGNNGNAGGPGAPGQAGQDGH 206
pGppGapGapGpp<-*
pG++GapGapG++
T10E10.1 207 PGNAGAPGAPGKV 219
Collagen: domain 3 of 4, from 223 to 229: score -3.8, E = 1.8e+03
*->pGapGpp<-*
pG++G+p
T10E10.1 223 PGPAGAP 229
Collagen: domain 4 of 4, from 230 to 289: score 49.4, E = 4.2e-12
*->GppGppGppGppGppGppGppGpaGapGppGppGepGpPGppGppGp
G+pGp Gp+Gp+G pG+pG pG +G++Gp+G+ G +G+PG+pG++G
T10E10.1 230 GAPGPDGPAGPAGSPGAPGNPGSQGPQGPAGDNGGAGSPGQPGANGD 276
pGppGapGapGpp<-*
G +G++GapG +
T10E10.1 277 NGADGEIGAPGGC 289