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/C31H2.2
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Query: C31H2.2 CE04130 locus:dpy-8 collagen alpha (weak) status:Partially_confirmed TR:Q18345 protein_id:AAA83336.1
Scores for sequence family classification (score includes all domains):
Model Description Score E-value N
-------- ----------- ----- ------- ---
Collagen Collagen triple helix repeat (20 copies 45.1 6.4e-11 4
Col_cuticle_N Nematode cuticle collagen N-terminal do 21.8 4.5e-05 1
hormone4 Neurohypophysial hormones, N-terminal D 5.5 8.9 1
DUF578 Protein of unknown function (DUF578) 3.4 8.3 1
Parsed for domains:
Model Domain seq-f seq-t hmm-f hmm-t score E-value
-------- ------- ----- ----- ----- ----- ----- -------
Col_cuticle_N 1/1 15 80 .. 1 66 [] 21.8 4.5e-05
hormone4 1/1 90 98 .. 1 9 [] 5.5 8.9
Collagen 1/4 96 127 .. 29 60 .] 16.5 0.0047
Collagen 2/4 144 203 .. 1 60 [] 37.1 1e-08
Collagen 3/4 209 230 .. 1 22 [. 9.9 0.3
Collagen 4/4 235 272 .. 5 42 .. 5.8 4.2
DUF578 1/1 424 451 .. 1 29 [. 3.4 8.3
Alignments of top-scoring domains:
Col_cuticle_N: domain 1 of 1, from 15 to 80: score 21.8, E = 4.5e-05
*->SgvAvlacLftvpsiyndInsfqdevmdemdeFKvyaddaWneMvdv
S++ +++++f+vp+++++ ++ e+ d K+++d +Wne++++
C31H2.2 15 STFTLVVAVFSVPMLFHKSDNVLLEISSFSDGIKAKSDLVWNELMEI 61
qrnvrppskpasarfgrpf<-*
++ p +++r++r
C31H2.2 62 KQGDAVPGIQYFSRKARSN 80
hormone4: domain 1 of 1, from 90 to 98: score 5.5, E = 8.9
*->CyirnCPrG<-*
C++ CP+G
C31H2.2 90 CFLLSCPQG 98
Collagen: domain 1 of 4, from 96 to 127: score 16.5, E = 0.0047
*->ppGppGepGpPGppGppGppGppGapGapGpp<-*
p+GppG+pG+PGp+G+pG +G +G++G+ G
C31H2.2 96 PQGPPGPPGAPGPDGQPGDAGRQGRSGDDGFD 127
Collagen: domain 2 of 4, from 144 to 203: score 37.1, E = 1e-08
*->GppGppGppGppGppGppGppGpaGapGppGppGepGpPGppGppGp
GppGp+G+ G++G++G+pG +G +G G+ G G pG PGppGp G
C31H2.2 144 GPPGPRGAQGERGMTGNPGMAGMQGTIGMEGVDGGPGLPGPPGPKGE 190
pGppGapGapGpp<-*
+Gp G+ G+pG
C31H2.2 191 RGPLGPYGPPGDT 203
Collagen: domain 3 of 4, from 209 to 230: score 9.9, E = 0.3
*->GppGppGppGppGppGppGppG<-*
G +Gp GppGp+G++GppGp G
C31H2.2 209 GIKGPLGPPGPQGMKGPPGPSG 230
Collagen: domain 4 of 4, from 235 to 272: score 5.8, E = 4.2
*->ppGppGppGppGppGppGpaGapGppGppGepGpPGpp<-*
+pG pG pG G G +G G+ G+ Gp+G+pG PG p
C31H2.2 235 QPGQPGQPGDIGGIGKTGKMGGYGMEGPAGPPGDPGMP 272
DUF578: domain 1 of 1, from 424 to 451: score 3.4, E = 8.3
*->agtlaEtieltaKwgknldsedhlrelrr<-*
a +++++++Kw+k l + lr+++r
C31H2.2 424 ANRMHDFQDFERKWRKKL-LQRRLRMMKR 451