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/F46C8.2
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Query: F46C8.2 CE04577 cuticle collagen status:Partially_confirmed TR:Q9GYP3 protein_id:AAF99941.1
Scores for sequence family classification (score includes all domains):
Model Description Score E-value N
-------- ----------- ----- ------- ---
Collagen Collagen triple helix repeat (20 copies 92.2 7.6e-24 3
Col_cuticle_N Nematode cuticle collagen N-terminal do 43.1 2.2e-11 1
Gas_vesicle_C Gas vesicles protein GVPc repeated doma 5.8 6.9 1
HesB-like HesB-like domain 4.8 3 1
Parsed for domains:
Model Domain seq-f seq-t hmm-f hmm-t score E-value
-------- ------- ----- ----- ----- ----- ----- -------
Gas_vesicle_C 1/1 13 22 .. 24 33 .] 5.8 6.9
Col_cuticle_N 1/1 30 92 .. 1 66 [] 43.1 2.2e-11
HesB-like 1/1 120 127 .. 104 111 .] 4.8 3
Collagen 1/3 126 160 .. 26 60 .] 15.2 0.011
Collagen 2/3 173 232 .. 1 60 [] 49.1 5.1e-12
Collagen 3/3 240 299 .. 1 60 [] 43.6 1.7e-10
Alignments of top-scoring domains:
Gas_vesicle_C: domain 1 of 1, from 13 to 22: score 5.8, E = 6.9
*->keQAeeLlqF<-*
+eQA +L++F
F46C8.2 13 QEQANSLRKF 22
Col_cuticle_N: domain 1 of 1, from 30 to 92: score 43.1, E = 2.2e-11
*->SgvAvlacLftvpsiyndInsfqdevmdemdeFKvyaddaWneMvdv
S++A l ++++vp +y+ ++++q+ ++ e+d+++ ++ ++W+e+ ++
F46C8.2 30 STIATLFSVISVPILYSVMQHMQSSMQSEVDFCRLRSGNIWRELSKT 76
qrnvrppskpasarfgrpf<-*
q+ + + a+ +++
F46C8.2 77 QILTQV---AGGAIVRSRR 92
HesB-like: domain 1 of 1, from 120 to 127: score 4.8, E = 3
*->CGCGkSFs<-*
CGCG S++
F46C8.2 120 CGCGVSPQ 127
Collagen: domain 1 of 3, from 126 to 160: score 15.2, E = 0.011
*->apGppGppGepGpPGppGppGppGppGapGapGpp<-*
++GppG pG +G G++G++G+pG +G++G++ p
F46C8.2 126 PQGPPGVPGRDGDNGADGEAGAPGKDGPDGPAATP 160
Collagen: domain 2 of 3, from 173 to 232: score 49.1, E = 5.1e-12
*->GppGppGppGppGppGppGppGpaGapGppGppGepGpPGppGppGp
GppGp+G++G Gp G+pG+pG +G++G++G +G+pG G+pG++G
F46C8.2 173 GPPGPAGSAGVKGPSGNPGAPGTDGPAGNKGGQGPPGNAGAPGANGN 219
pGppGapGapGpp<-*
pG++G pG pG+
F46C8.2 220 PGNAGTPGIPGKT 232
Collagen: domain 3 of 3, from 240 to 299: score 43.6, E = 1.7e-10
*->GppGppGppGppGppGppGppGpaGapGppGppGepGpPGppGppGp
Gp+G pGp+GppG +G pG +G++G+ G+pG++G++G G+pG+pG
F46C8.2 240 GPAGAPGPAGPPGTAGTPGSQGQPGKDGSPGDAGDNGTAGSPGHPGG 286
pGppGapGapGpp<-*
Gp G++Ga Gp
F46C8.2 287 EGPVGPDGARGPS 299