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/F56B3.1
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Query: F56B3.1 CE17882 status:Confirmed TR:O45114 protein_id:AAK29827.1
Scores for sequence family classification (score includes all domains):
Model Description Score E-value N
-------- ----------- ----- ------- ---
Col_cuticle_N Nematode cuticle collagen N-terminal do 77.1 1.7e-21 1
Collagen Collagen triple helix repeat (20 copies 64.1 3.9e-16 3
Parsed for domains:
Model Domain seq-f seq-t hmm-f hmm-t score E-value
-------- ------- ----- ----- ----- ----- ----- -------
Col_cuticle_N 1/1 15 71 .. 1 66 [] 77.1 1.7e-21
Collagen 1/3 141 175 .. 26 60 .] 17.7 0.0022
Collagen 2/3 188 247 .. 1 60 [] 31.7 3.2e-07
Collagen 3/3 256 315 .. 1 60 [] 31.0 5e-07
Alignments of top-scoring domains:
Col_cuticle_N: domain 1 of 1, from 15 to 71: score 77.1, E = 1.7e-21
*->SgvAvlacLftvpsiyndInsfqdevmdemdeFKvyaddaWneMvdv
Sgv +lacLf++++++nd+ns++devm++md+FKv+++ aW+ + dv
F56B3.1 15 SGVTILACLFFAAQVFNDVNSLYDEVMVDMDAFKVKSNIAWEAINDV 61
qrnvrppskpasarfgrpf<-*
+++ r+ +r++
F56B3.1 62 IAPNRE---------KRGY 71
Collagen: domain 1 of 3, from 141 to 175: score 17.7, E = 0.0022
*->apGppGppGepGpPGppGppGppGppGapGapGpp<-*
+pGp+GppG +G +G pG+pG+pG G +G+ G+
F56B3.1 141 PPGPRGPPGQAGLDGLPGAPGQPGSNGGAGSNGAS 175
Collagen: domain 2 of 3, from 188 to 247: score 31.7, E = 3.2e-07
*->GppGppGppGppGppGppGppGpaGapGppGppGepGpPGppGppGp
GppGppGp+G +G pG+ G+pG++ + G G+pG+pGp G +G pG+
F56B3.1 188 GPPGPPGPAGQAGRPGNDGQPGAPSFGGGVGAPGAPGPAGDAGSPGQ 234
pGppGapGapGpp<-*
pG pG+pG pG++
F56B3.1 235 PGAPGQPGRPGKN 247
Collagen: domain 3 of 3, from 256 to 315: score 31.0, E = 5e-07
*->GppGppGppGppGppGppGppGpaGapGppGppGepGpPGppGppGp
GppGp+GppGppG G+pG G+pGppGp+G pG+PG+pGp+G+
F56B3.1 256 GPPGPAGPPGPPGNNGAPGGGYGVGPPGPPGPSGRPGAPGQPGPDGQ 302
pGppGapGapGpp<-*
pG pG++G pG
F56B3.1 303 PGAPGNDGTPGTD 315