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/F41C6.5
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Query: F41C6.5 CE04542 cuticular collagen status:Partially_confirmed TR:Q20270 protein_id:AAA80446.1
Scores for sequence family classification (score includes all domains):
Model Description Score E-value N
-------- ----------- ----- ------- ---
Collagen Collagen triple helix repeat (20 copies 69.7 1.2e-17 3
Col_cuticle_N Nematode cuticle collagen N-terminal do 22.2 3.4e-05 1
Parsed for domains:
Model Domain seq-f seq-t hmm-f hmm-t score E-value
-------- ------- ----- ----- ----- ----- ----- -------
Col_cuticle_N 1/1 29 87 .. 1 66 [] 22.2 3.4e-05
Collagen 1/3 135 164 .. 31 60 .] 21.1 0.00026
Collagen 2/3 185 243 .. 1 60 [] 25.5 1.6e-05
Collagen 3/3 249 307 .. 1 60 [] 38.5 4.2e-09
Alignments of top-scoring domains:
Col_cuticle_N: domain 1 of 1, from 29 to 87: score 22.2, E = 3.4e-05
*->SgvAvlacLftvpsiyndInsfqdevmdemdeFKvyaddaWneMvdv
S+ A ++c+ tvp++yn+++ ++ +++e d+++++ d + +e++ +
F41C6.5 29 SIGAAIVCVMTVPFVYNYVQRVETVLQNEADFCRAKRDSVLKELTRT 75
qrnvrppskpasarfgrpf<-*
q ++ r++r
F41C6.5 76 QKRAG-------LRLKRED 87
Collagen: domain 1 of 3, from 135 to 164: score 21.1, E = 0.00026
*->GppGepGpPGppGppGppGppGapGapGpp<-*
G pGepG+PG++G++G G pG +G pG+
F41C6.5 135 GSPGEPGSPGQDGHDGVDGRPGSDGNPGAD 164
Collagen: domain 2 of 3, from 185 to 243: score 25.5, E = 1.6e-05
*->GppGppGppGppGppGppGppGpaGapGppGppGepGpPGppGppGp
p GppGppG+ G+pG pG +G++ +pG +G pG+ GpPGp+GppG
F41C6.5 185 -PTGPPGPPGLKGMPGIPGNQGEDAGPGRQGMPGPTGPPGPRGPPGE 230
pGppGapGapGpp<-*
G +G+ G+ G p
F41C6.5 231 TGDEGEGGPDGIP 243
Collagen: domain 3 of 3, from 249 to 307: score 38.5, E = 4.2e-09
*->GppGppGppGppGppGppGppGpaGapGppGppGepGpPGppGppGp
ppGp+GppGp+Gp+Gp Gp G +G++GppGp G G+ G G+pG
F41C6.5 249 -PPGPRGPPGPAGPDGPQGPEGRSGKQGPPGPTGQEGEEGVIGEPGK 294
pGppGapGapGpp<-*
pG+pG++Ga+G++
F41C6.5 295 PGEPGKSGAAGAR 307