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: hmm3/seq/F59F3.2
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Query: F59F3.2 CE18797 collagen status:Partially_confirmed TR:Q21039 protein_id:CAA91992.1
Scores for sequence family classification (score includes all domains):
Model Description Score E-value N
-------- ----------- ----- ------- ---
Collagen Collagen triple helix repeat (20 copies) 51.6 1.1e-12 4
Parsed for domains:
Model Domain seq-f seq-t hmm-f hmm-t score E-value
-------- ------- ----- ----- ----- ----- ----- -------
Collagen 1/4 24 53 .. 14 43 .. 3.1 23
Collagen 2/4 63 97 .. 26 60 .] 20.4 0.00041
Collagen 3/4 98 126 .. 11 39 .. 11.3 0.13
Collagen 4/4 132 191 .. 1 60 [] 39.7 1.9e-09
Alignments of top-scoring domains:
Collagen: domain 1 of 4, from 24 to 53: score 3.1, E = 23
*->ppGppGppGpaGapGppGppGepGpPGppG<-*
p+Gp+GppG++G G+pG++G +G +G
F59F3.2 24 PKGPRGPPGDDGNSPTDGHPGDNGKDGTDG 53
Collagen: domain 2 of 4, from 63 to 97: score 20.4, E = 0.00041
*->apGppGppGepGpPGppGppGppGppGapGapGpp<-*
+p p+GppGe+G G +G+pG pG pG pG pG +
F59F3.2 63 PPCPQGPPGEDGLRGEAGEPGRPGTPGDPGRPGTN 97
Collagen: domain 3 of 4, from 98 to 126: score 11.3, E = 0.13
*->ppGppGppGppGpaGapGppGppGepGpP<-*
+pG G++Gp G++G G++G+pGe+G++
F59F3.2 98 EPGGIGARGPRGQSGRTGSKGDPGEAGQD 126
Collagen: domain 4 of 4, from 132 to 191: score 39.7, E = 1.9e-09
*->GppGppGppGppGppGppGppGpaGapGppGppGepGpPGppGppGp
G pGp G pG G pG++G pG++G+p ppGp G+pGp G G +G
F59F3.2 132 GLPGPKGLPGSVGLPGARGDPGNNGKPAPPGPEGFPGPVGDLGDAGE 178
pGppGapGapGpp<-*
G +G pG G p
F59F3.2 179 YGLRGVPGRRGSP 191