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/F38A3.2
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Query: F38A3.2 CE02214 collagen status:Confirmed TR:Q20136 protein_id:CAA90188.1
Scores for sequence family classification (score includes all domains):
Model Description Score E-value N
-------- ----------- ----- ------- ---
Collagen Collagen triple helix repeat (20 copies 106.8 4.1e-28 3
Col_cuticle_N Nematode cuticle collagen N-terminal do 41.2 8e-11 1
Flavi_NS4A Flavivirus non-structural protein NS4A 4.1 1.8 1
Parsed for domains:
Model Domain seq-f seq-t hmm-f hmm-t score E-value
-------- ------- ----- ----- ----- ----- ----- -------
Flavi_NS4A 1/1 19 36 .. 132 149 .] 4.1 1.8
Col_cuticle_N 1/1 28 65 .. 1 38 [. 41.2 8e-11
Collagen 1/3 115 149 .. 26 60 .] 17.0 0.0034
Collagen 2/3 165 224 .. 1 60 [] 53.7 2.9e-13
Collagen 3/3 232 291 .. 1 60 [] 52.4 6.6e-13
Alignments of top-scoring domains:
Flavi_NS4A: domain 1 of 1, from 19 to 36: score 4.1, E = 1.8
*->qLAyllIgilTlVgaVAA<-*
++A++ I+i T++ ++A
F38A3.2 19 KVAFFGICISTVATLTAI 36
Col_cuticle_N: domain 1 of 1, from 28 to 65: score 41.2, E = 8e-11
*->SgvAvlacLftvpsiyndInsfqdevmdemdeFKvyad<-*
S+vA l++++++p +yn++++ q++++ e+d++K++++
F38A3.2 28 STVATLTAIVAIPLLYNYMQHVQSTLQTEVDFCKHRTN 65
Collagen: domain 1 of 3, from 115 to 149: score 17.0, E = 0.0034
*->apGppGppGepGpPGppGppGppGppGapGapGpp<-*
++G GppG+pG +G++G++G Gp+G+pGa p
F38A3.2 115 KAGASGPPGPPGTDGSDGKDGLSGPDGQPGADADP 149
Collagen: domain 2 of 3, from 165 to 224: score 53.7, E = 2.9e-13
*->GppGppGppGppGppGppGppGpaGapGppGppGepGpPGppGppGp
GppGp+G pGp Gp G++G+ G++GapG++G++G+pG+PGp+Gp+G+
F38A3.2 165 GPPGPAGNPGPKGPSGNAGADGQPGAPGNAGAAGAPGAPGPAGPDGQ 211
pGppGapGapGpp<-*
pG +G++GapG +
F38A3.2 212 PGSTGQDGAPGVV 224
Collagen: domain 3 of 3, from 232 to 291: score 52.4, E = 6.6e-13
*->GppGppGppGppGppGppGppGpaGapGppGppGepGpPGppGppGp
Gp+G pGp+G+pG++G++G+pG++G Gp+Gp+G++G++G++G+pG+
F38A3.2 232 GPAGAPGPAGAPGADGAAGAPGQPGQDGPQGPAGDAGSDGAAGQPGA 278
pGppGapGapGpp<-*
+G++G++G+pG+
F38A3.2 279 AGEQGPAGEPGAG 291