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: hmm5/seq/Y57A10A.11
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Query: Y57A10A.11 CE22614 locus:rol-1 status:Partially_confirmed TR:Q9NA83 protein_id:CAB55014.1
Scores for sequence family classification (score includes all domains):
Model Description Score E-value N
-------- ----------- ----- ------- ---
Collagen Collagen triple helix repeat (20 copies 82.7 3.1e-21 3
Col_cuticle_N Nematode cuticle collagen N-terminal do 23.4 1.6e-05 1
Parsed for domains:
Model Domain seq-f seq-t hmm-f hmm-t score E-value
-------- ------- ----- ----- ----- ----- ----- -------
Col_cuticle_N 1/1 21 82 .. 1 66 [] 23.4 1.6e-05
Collagen 1/3 261 294 .. 27 60 .] 19.9 0.00055
Collagen 2/3 308 366 .. 1 60 [] 35.0 3.9e-08
Collagen 3/3 375 434 .. 1 60 [] 43.6 1.7e-10
Alignments of top-scoring domains:
Col_cuticle_N: domain 1 of 1, from 21 to 82: score 23.4, E = 1.6e-05
*->SgvAvlacLftvpsiyndInsfqdevmdemdeFKvyaddaWneMvdv
S++A++a ++t+p + +I + q + em+ ++ +a W+++ +
Y57A10A.11 21 STLAIIALCVTLPIVHGYIKEVQHSMKIEMNQCQNNAKTLWTDVYML 67
qrnvrppskpasarfgrpf<-*
+++ + ++r++r+
Y57A10A.11 68 RASFTRG----FNRTARQA 82
Collagen: domain 1 of 3, from 261 to 294: score 19.9, E = 0.00055
*->pGppGppGepGpPGppGppGppGppGapGapGpp<-*
pGp+GppG+pG+PGppG++G+ G pG++G p ++
Y57A10A.11 261 PGPAGPPGAPGRPGPPGKAGANGLPGNSGKPTKR 294
Collagen: domain 2 of 3, from 308 to 366: score 35.0, E = 3.9e-08
*->GppGppGppGppGppGppGppGpaGapGppGppGepGpPGppGppGp
p Gp Gp+Gp+Gp G+ G pG G++Gp+Gp G+pG+ G +G+ G
Y57A10A.11 308 -PQGPLGPAGPAGPQGNLGGPGVFGEKGPQGPVGAPGQKGRRGEKGK 353
pGppGapGapGpp<-*
G+pGapGapG++
Y57A10A.11 354 DGEPGAPGAPGEN 366
Collagen: domain 3 of 3, from 375 to 434: score 43.6, E = 1.7e-10
*->GppGppGppGppGppGppGppGpaGapGppGppGepGpPGppGppGp
Gp G pGp+G +Gp+G+pG pG +G G++G+pGepG++G pG +G
Y57A10A.11 375 GPQGTPGPRGRQGPRGAPGIPGKDGLGGDQGAPGEPGADGEPGMDGV 421
pGppGapGapGpp<-*
pG+pG++G G
Y57A10A.11 422 PGNPGRDGTHGHG 434