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/C01B12.1
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Query: C01B12.1 CE07789 cuticular collagen status:Partially_confirmed TR:O17209 protein_id:AAB70974.1
Scores for sequence family classification (score includes all domains):
Model Description Score E-value N
-------- ----------- ----- ------- ---
Col_cuticle_N Nematode cuticle collagen N-terminal do 54.3 9.6e-15 1
Collagen Collagen triple helix repeat (20 copies 50.3 2.5e-12 4
Parsed for domains:
Model Domain seq-f seq-t hmm-f hmm-t score E-value
-------- ------- ----- ----- ----- ----- ----- -------
Col_cuticle_N 1/1 21 77 .. 1 66 [] 54.3 9.6e-15
Collagen 1/4 108 141 .. 23 56 .. 10.2 0.26
Collagen 2/4 158 215 .. 1 58 [. 29.9 9.9e-07
Collagen 3/4 222 248 .. 34 60 .] 15.1 0.012
Collagen 4/4 251 286 .. 25 60 .] 18.8 0.0011
Alignments of top-scoring domains:
Col_cuticle_N: domain 1 of 1, from 21 to 77: score 54.3, E = 9.6e-15
*->SgvAvlacLftvpsiyndInsfqdevmdemdeFKvyaddaWneMvdv
S+vAv+a+++ +p++y+++ fq++++ e d++K++++d+W ++ d+
C01B12.1 21 STVAVIAAIVILPMLYSYVAGFQSHLIIEADFCKTRSRDMWAQIHDI 67
qrnvrppskpasarfgrpf<-*
+ f r++
C01B12.1 68 DGPHL---------FHRQK 77
Collagen: domain 1 of 4, from 108 to 141: score 10.2, E = 0.26
*->paGapGppGppGepGpPGppGppGppGppGapGa<-*
++G++GppGppG++G G++G+ G G +G+ G+
C01B12.1 108 QQGPAGPPGPPGDDGNGGQDGVRGNDGTDGKEGS 141
Collagen: domain 2 of 4, from 158 to 215: score 29.9, E = 9.9e-07
*->GppGppGppGppGppGppGppGpaGapGppGppGepGpPGppGppGp
GppGp+G +G+ Gp Gp+G G++G+ G +G+ G GpPG GppG
C01B12.1 158 GPPGPQGMAGAKGPQGPKGGNGDNGPDGKAGANGMQGPPGMMGPPGR 204
pGppGapGapG<-*
+G G++GapG
C01B12.1 205 QGVSGPKGAPG 215
Collagen: domain 3 of 4, from 222 to 248: score 15.1, E = 0.012
*->GepGpPGppGppGppGppGapGapGpp<-*
G++Gp G++G+ GppGp+G++G G +
C01B12.1 222 GPAGPAGHKGVRGPPGPRGEAGLDGGN 248
Collagen: domain 4 of 4, from 251 to 286: score 18.8, E = 0.0011
*->GapGppGppGepGpPGppGppGppGppGapGapGpp<-*
G++Gp+G++G pGp G +Gp Gp Gp+G+pG+pG +
C01B12.1 251 GPQGPQGDAGRPGPVGEQGPQGPEGPQGPPGEPGGC 286