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/T07H6.3
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Query: T07H6.3 CE04913 collagen status:Partially_confirmed TR:Q22326 protein_id:AAA96223.1
Scores for sequence family classification (score includes all domains):
Model Description Score E-value N
-------- ----------- ----- ------- ---
Collagen Collagen triple helix repeat (20 copies 107.6 2.3e-28 3
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 87 150 .. 1 66 [] 56.6 2.1e-15
Collagen 1/3 175 209 .. 26 60 .] 20.1 0.00048
Collagen 2/3 222 281 .. 1 60 [] 56.3 5.6e-14
Collagen 3/3 289 348 .. 1 60 [] 47.1 1.8e-11
Alignments of top-scoring domains:
Col_cuticle_N: domain 1 of 1, from 87 to 150: score 56.6, E = 2.1e-15
*->SgvAvlacLftvpsiyndInsfqdevmdemdeFKvyaddaWneMvdv
S A l+c++++p++yn+++++q+ ++ e+d+++ ++ ++W+e++ +
T07H6.3 87 SFTATLVCVIAAPMLYNYMQHMQSVMQSEVDFCRSRSGNIWREVTRT 133
qrnvrppskpasarfgrpf<-*
q+ + + + r +r+
T07H6.3 134 QVLAKVS--GGALRSRRQA 150
Collagen: domain 1 of 3, from 175 to 209: score 20.1, E = 0.00048
*->apGppGppGepGpPGppGppGppGppGapGapGpp<-*
a+GppG+pG +G++G++G+pG+pG++G++G++ p
T07H6.3 175 AAGPPGAPGSDGEDGADGQPGAPGNDGPDGPAATP 209
Collagen: domain 2 of 3, from 222 to 281: score 56.3, E = 5.6e-14
*->GppGppGppGppGppGppGppGpaGapGppGppGepGpPGppGppGp
GppGp+Gp+Gp Gp G++G G++GapG++G++G pG+PG++G++G
T07H6.3 222 GPPGPAGPAGPKGPNGNSGSDGQPGAPGNNGNAGGPGAPGQAGQDGH 268
pGppGapGapGpp<-*
pG++GapGapG++
T07H6.3 269 PGNAGAPGAPGKV 281
Collagen: domain 3 of 3, from 289 to 348: score 47.1, E = 1.8e-11
*->GppGppGppGppGppGppGppGpaGapGppGppGepGpPGppGppGp
G+pG pGp Gp+Gp+G pG+pG++G++Gp+Gp+G++G G+pG+pG+
T07H6.3 289 GAPGAPGPDGPAGPAGSPGAPGNPGSQGPQGPAGDNGGAGSPGQPGA 335
pGppGapGapGpp<-*
G Ga+G+ G+p
T07H6.3 336 NGDNGADGETGAP 348