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: hmm2/seq/F27C1.8
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Query: F27C1.8 CE09720 cuticular collagen status:Partially_confirmed SW:P91285 protein_id:AAB37656.1
Scores for sequence family classification (score includes all domains):
Model Description Score E-value N
-------- ----------- ----- ------- ---
Collagen Collagen triple helix repeat (20 copies 88.4 8.3e-23 3
Col_cuticle_N Nematode cuticle collagen N-terminal do 70.3 1.7e-19 1
Parsed for domains:
Model Domain seq-f seq-t hmm-f hmm-t score E-value
-------- ------- ----- ----- ----- ----- ----- -------
Col_cuticle_N 1/1 13 74 .. 1 66 [] 70.3 1.7e-19
Collagen 1/3 95 124 .. 23 52 .. 9.6 0.38
Collagen 2/3 141 199 .. 1 60 [] 42.9 2.7e-10
Collagen 3/3 214 273 .. 1 60 [] 52.5 5.9e-13
Alignments of top-scoring domains:
Col_cuticle_N: domain 1 of 1, from 13 to 74: score 70.3, E = 1.7e-19
*->SgvAvlacLftvpsiyndInsfqdevmdemdeFKvyaddaWneMvdv
+ A++acL+++++i ndIn+++d+vm+e++ F++++dd+W +++dv
F27C1.8 13 GISAIVACLWAALVITNDINDMYDDVMGELGGFRDISDDTWGTLLDV 59
qrnvrppskpasarfgrpf<-*
+ +++++ +++++r+
F27C1.8 60 RHGAGES----AEQYVRGI 74
Collagen: domain 1 of 3, from 95 to 124: score 9.6, E = 0.38
*->paGapGppGppGepGpPGppGppGppGppG<-*
paGapG+pG+pGepG Gp+G++Gp G pG
F27C1.8 95 PAGAPGNPGAPGEPGGTGPDGKNGPTGLPG 124
Collagen: domain 2 of 3, from 141 to 199: score 42.9, E = 2.7e-10
*->GppGppGppGppGppGppGppGpaGapGppGppGepGpPGppGppGp
p+GppG G+pG+ G G pG+aG++G pG GepG+ G G G
F27C1.8 141 -PAGPPGQDGLPGQEGFQGLPGDAGKRGTPGKDGEPGRVGDIGDQGT 186
pGppGapGapGpp<-*
pG++G+pG +Gpp
F27C1.8 187 PGQDGQPGLAGPP 199
Collagen: domain 3 of 3, from 214 to 273: score 52.5, E = 5.9e-13
*->GppGppGppGppGppGppGppGpaGapGppGppGepGpPGppGppGp
G+pG pGp+G+pG G+pG+ G+ Ga+Gp G pG +G+ G +G pG+
F27C1.8 214 GRPGMPGPRGEPGNNGNPGEEGQTGAQGPTGQPGKDGFNGNDGTPGQ 260
pGppGapGapGpp<-*
+Gp+Ga Ga +
F27C1.8 261 AGPQGAVGADAEY 273