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: hmm4/seq/T01B7.7
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Query: T01B7.7 CE03591 locus:rol-6 cuticle collagen ROL-6 status:Partially_confirmed SW:P20784 protein_id:CAA91300.1
Scores for sequence family classification (score includes all domains):
Model Description Score E-value N
-------- ----------- ----- ------- ---
Collagen Collagen triple helix repeat (20 copies 80.5 1.2e-20 3
Col_cuticle_N Nematode cuticle collagen N-terminal do 61.3 8.2e-17 1
Parsed for domains:
Model Domain seq-f seq-t hmm-f hmm-t score E-value
-------- ------- ----- ----- ----- ----- ----- -------
Col_cuticle_N 1/1 14 73 .. 1 66 [] 61.3 8.2e-17
Collagen 1/3 150 184 .. 26 60 .] 20.3 0.00042
Collagen 2/3 199 258 .. 1 60 [] 44.9 7.3e-11
Collagen 3/3 261 320 .. 1 60 [] 30.0 9.4e-07
Alignments of top-scoring domains:
Col_cuticle_N: domain 1 of 1, from 14 to 73: score 61.3, E = 8.2e-17
*->SgvAvlacLftvpsiyndInsfqdevmdemdeFKvyaddaWneMvdv
Sg+ +l++Lf+++s+y+++++++ e++ e+ +F+ ++ d+W +Mv++
T01B7.7 14 SGATLLVSLFAAASLYSQVSNIWNELDAEIANFRSLTEDMWVDMVKL 60
qrnvrppskpasarfgrpf<-*
++++ s+r +r+
T01B7.7 61 GAGTA------SNRVRRQQ 73
Collagen: domain 1 of 3, from 150 to 184: score 20.3, E = 0.00042
*->apGppGppGepGpPGppGppGppGppGapGapGpp<-*
+pGp+Gp Ge Gp+G++G++G pG +G++ + ++
T01B7.7 150 PPGPAGPEGEEGPDGHDGQDGVPGFDGKDAEDVQN 184
Collagen: domain 2 of 3, from 199 to 258: score 44.9, E = 7.3e-11
*->GppGppGppGppGppGppGppGpaGapGppGppGepGpPGppGppGp
Gp Gp G+pG++G++G++G+pG +G G+pG pG+ GpPG+pG +G
T01B7.7 199 GPQGPNGAPGLRGMRGARGQPGRPGRDGNPGMPGDCGPPGAPGSDGK 245
pGppGapGapGpp<-*
pG pG +G+ G++
T01B7.7 246 PGSPGGKGDDGER 258
Collagen: domain 3 of 3, from 261 to 320: score 30.0, E = 9.4e-07
*->GppGppGppGppGppGppGppGpaGapGppGppGepGpPGppGppGp
G+pGp+GppG++Gp Gp Gp+G + pG Gp+GepG +G G++G
T01B7.7 261 GRPGPRGPPGEAGPEGPQGPTGRDAYPGQSGPQGEPGLQGYGGAAGE 307
pGppGapGapGpp<-*
Gp+G+pGapG p
T01B7.7 308 DGPEGPPGAPGLP 320