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: hmm2/seq/C50D2.4
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Query: C50D2.4 CE08889 cuticular collagen status:Partially_confirmed TR:O44796 protein_id:AAB94952.1
Scores for sequence family classification (score includes all domains):
Model Description Score E-value N
-------- ----------- ----- ------- ---
Collagen Collagen triple helix repeat (20 copies 79.6 2.2e-20 4
Col_cuticle_N Nematode cuticle collagen N-terminal do 45.2 5e-12 1
Flavi_NS4A Flavivirus non-structural protein NS4A 2.9 4.8 1
Parsed for domains:
Model Domain seq-f seq-t hmm-f hmm-t score E-value
-------- ------- ----- ----- ----- ----- ----- -------
Flavi_NS4A 1/1 22 39 .. 132 149 .] 2.9 4.8
Col_cuticle_N 1/1 31 88 .. 1 66 [] 45.2 5e-12
Collagen 1/4 141 170 .. 31 60 .] 19.4 0.00078
Collagen 2/4 189 248 .. 1 60 [] 48.0 1e-11
Collagen 3/4 253 278 .. 1 26 [. 14.4 0.018
Collagen 4/4 281 311 .. 30 60 .] 21.8 0.00017
Alignments of top-scoring domains:
Flavi_NS4A: domain 1 of 1, from 22 to 39: score 2.9, E = 4.8
*->qLAyllIgilTlVgaVAA<-*
+LA++ I+i T++ ++A
C50D2.4 22 KLAFFGIAISTVATLTAI 39
Col_cuticle_N: domain 1 of 1, from 31 to 88: score 45.2, E = 5e-12
*->SgvAvlacLftvpsiyndInsfqdevmdemdeFKvyaddaWneMvdv
S+vA l+++ +vp++yn++++ q+ ++ e+d+++++++ W+e +
C50D2.4 31 STVATLTAIMAVPMLYNYMQHVQSALQSEVDFCRHRTNGLWDEYNKF 77
qrnvrppskpasarfgrpf<-*
++ ++ ++r +
C50D2.4 78 ESVAGV--------RRRIK 88
Collagen: domain 1 of 4, from 141 to 170: score 19.4, E = 0.00078
*->GppGepGpPGppGppGppGppGapGapGpp<-*
GppG++G+PG +G pG G pG+pG pG+
C50D2.4 141 GPPGPSGAPGTDGNPGNDGSPGNPGTPGQD 170
Collagen: domain 2 of 4, from 189 to 248: score 48.0, E = 1e-11
*->GppGppGppGppGppGppGppGpaGapGppGppGepGpPGppGppGp
GppGppG Gp Gp G+pG+pG +G+ pGppG+pGp+GppG++G
C50D2.4 189 GPPGPPGKQGPKGPNGEPGAPGTPGGNALPGPPGPPGPQGPPGADGL 235
pGppGapGapGpp<-*
pG+pGapG pG++
C50D2.4 236 PGNPGAPGVPGQV 248
Collagen: domain 3 of 4, from 253 to 278: score 14.4, E = 0.018
*->GppGppGppGppGppGppGppGpaGa<-*
G pGp+GppGppGp GppG+pG++G+
C50D2.4 253 GTPGPAGPPGPPGPIGPPGQPGAPGS 278
Collagen: domain 4 of 4, from 281 to 311: score 21.8, E = 0.00017
*->pGppGepGpPGppGppGppGppGapGapGpp<-*
pGp+G+pG PG +G+pG pG pG+pG+pG+p
C50D2.4 281 PGPQGPPGDPGIDGAPGNPGSPGEPGPPGQP 311