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/C15A11.5
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Query: C15A11.5 CE08173 locus:col-7 collagen status:Partially_confirmed SW:P18832 protein_id:CAB01961.1
Scores for sequence family classification (score includes all domains):
Model Description Score E-value N
-------- ----------- ----- ------- ---
Col_cuticle_N Nematode cuticle collagen N-terminal do 84.4 1.1e-23 1
Collagen Collagen triple helix repeat (20 copies 78.5 4.5e-20 3
7tm_1 7 transmembrane receptor (rhodopsin fam 2.7 2.8 1
Parsed for domains:
Model Domain seq-f seq-t hmm-f hmm-t score E-value
-------- ------- ----- ----- ----- ----- ----- -------
Col_cuticle_N 1/1 14 75 .. 1 66 [] 84.4 1.1e-23
Collagen 1/3 92 126 .. 26 60 .] 19.8 0.00058
Collagen 2/3 139 198 .. 1 60 [] 35.7 2.5e-08
Collagen 3/3 204 263 .. 1 60 [] 38.8 3.6e-09
7tm_1 1/1 65 304 .. 186 212 .. 2.7 2.8
Alignments of top-scoring domains:
Col_cuticle_N: domain 1 of 1, from 14 to 75: score 84.4, E = 1.1e-23
*->SgvAvlacLftvpsiyndInsfqdevmdemdeFKvyaddaWneMvdv
Sg++v+++L++v++iy+dInsf +++++e++eFK++a+daWn+M++
C15A11.5 14 SGIVVFGALISVFHIYSDINSFVEDSHRELGEFKGFANDAWNSMINQ 60
qrnvrppskpasarfgrpf<-*
++vr+ a++ fgr+
C15A11.5 61 DDSVRM----ARSVFGRRR 75
Collagen: domain 1 of 3, from 92 to 126: score 19.8, E = 0.00058
*->apGppGppGepGpPGppGppGppGppGapGapGpp<-*
++GppGppG++G G++G+pG++G pG+pG +Gp
C15A11.5 92 PAGPPGPPGASGDKGHDGQPGQAGKPGQPGVAGPS 126
Collagen: domain 2 of 3, from 139 to 198: score 35.7, E = 2.5e-08
*->GppGppGppGppGppGppGppGpaGapGppGppGepGpPGppGppGp
G pGp+G pG pGp+Gp G pG++ G +GppG+pGp G++G pG+
C15A11.5 139 GLPGPAGVPGQPGPKGPNGNPGAPAQGGGQGPPGPPGPAGSAGSPGQ 185
pGppGapGapGpp<-*
+G pG+pG+pG+
C15A11.5 186 AGAPGNPGSPGKS 198
Collagen: domain 3 of 3, from 204 to 263: score 38.8, E = 3.6e-09
*->GppGppGppGppGppGppGppGpaGapGppGppGepGpPGppGppGp
G pGp G+pGp+GppG+pG+pG apGp+GppG++Gp G+pG+pG+
C15A11.5 204 GLPGPSGAPGPQGPPGAPGQPGSGNAPGPAGPPGPAGPNGQPGHPGQ 250
pGppGapGapGpp<-*
G+pGapG G p
C15A11.5 251 DGQPGAPGNDGTP 263
7tm_1: domain 1 of 1, from 65 to 304: score 2.7, E = 2.8
*->rIlrtlrkrarkgas................................
r++r ++ r+r+ ++++ + +++ ++ + +++++++ ++++++++++
C15A11.5 65 RMARSVFGRRRQKKQsqcncgqqasncpagppgppgasgdkghdgqp 111
..................................................
++ +++++++ +++++++++ + +++ +++ + ++++++++++++++
C15A11.5 112 gqagkpgqpgvagpshhqkqecikcpqglpgpagvpgqpgpkgpngnpga 161
..................................................
+ +++++++++++++ ++ +++++ + ++++++++++++++++ +++++
C15A11.5 162 paqgggqgppgppgpagsagspgqagapgnpgspgksgqrgrglpgpsga 211
..................................................
++++++++ ++++++++ +++ +++++ ++++++++++++++++ +++++
C15A11.5 212 pgpqgppgapgqpgsgnapgpagppgpagpngqpghpgqdgqpgapgndg 261
...............................kkrsskerkaak<-*
+++++ + +++++ ++++ ++++ +kkr+ +++++ak
C15A11.5 262 tpgsdaaycpcptrssvlrhrnvnrhraaasKKRVVAKKRVAK 304