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/F11G11.12
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Query: F11G11.12 CE09354 collagen status:Partially_confirmed TR:P91250 protein_id:AAB37843.1
Scores for sequence family classification (score includes all domains):
Model Description Score E-value N
-------- ----------- ----- ------- ---
Collagen Collagen triple helix repeat (20 copies 103.5 4.2e-27 3
Col_cuticle_N Nematode cuticle collagen N-terminal do 30.6 1.1e-07 1
Parsed for domains:
Model Domain seq-f seq-t hmm-f hmm-t score E-value
-------- ------- ----- ----- ----- ----- ----- -------
Col_cuticle_N 1/1 26 63 .. 1 38 [. 30.6 1.1e-07
Collagen 1/3 95 124 .. 31 60 .] 16.7 0.0041
Collagen 2/3 144 203 .. 1 60 [] 47.6 1.3e-11
Collagen 3/3 211 270 .. 1 60 [] 54.8 1.4e-13
Alignments of top-scoring domains:
Col_cuticle_N: domain 1 of 1, from 26 to 63: score 30.6, E = 1.1e-07
*->SgvAvlacLftvpsiyndInsfqdevmdemdeFKvyad<-*
S+vA l+++++vp++ ++++ q+ ++de++++++++d
F11G11.12 26 STVATLTAIVAVPMLCMYMQNVQSGLQDEINFCRTRSD 63
Collagen: domain 1 of 3, from 95 to 124: score 16.7, E = 0.0041
*->GppGepGpPGppGppGppGppGapGapGpp<-*
Gp+G G PG++G+pG G pGapGapGp
F11G11.12 95 GPAGSVGNPGQDGAPGNDGRPGAPGAPGPD 124
Collagen: domain 2 of 3, from 144 to 203: score 47.6, E = 1.3e-11
*->GppGppGppGppGppGppGppGpaGapGppGppGepGpPGppGppGp
Gp+G +G pGp GppG pG+pG++G+ G pG+pG+pGp+GppG +G
F11G11.12 144 GPAGNAGNPGPKGPPGQPGAPGEQGPNGRPGAPGAPGPQGPPGTAGN 190
pGppGapGapGpp<-*
G pG+pGapG++
F11G11.12 191 DGTPGQPGAPGQV 203
Collagen: domain 3 of 3, from 211 to 270: score 54.8, E = 1.4e-13
*->GppGppGppGppGppGppGppGpaGapGppGppGepGpPGppGppGp
G pG+pG+pG++GppG+ G pG++G++GppGp+GepG++G+pG pG+
F11G11.12 211 GNPGQPGEPGAQGPPGEDGRPGNSGPQGPPGPQGEPGQDGAPGNPGA 257
pGppGapGapGpp<-*
pG++G+pG G+
F11G11.12 258 PGEAGEPGKDGAK 270