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: hmm1/seq/C39E9.3
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Query: C39E9.3 CE05386 collagen status:Partially_confirmed TR:Q18537 protein_id:CAA94329.1
Scores for sequence family classification (score includes all domains):
Model Description Score E-value N
-------- ----------- ----- ------- ---
Collagen Collagen triple helix repeat (20 copies 68.6 2.2e-17 3
Col_cuticle_N Nematode cuticle collagen N-terminal do 7.1 1.1 1
B56 Protein phosphatase 2A regulatory B sub 2.5 5.5 1
Parsed for domains:
Model Domain seq-f seq-t hmm-f hmm-t score E-value
-------- ------- ----- ----- ----- ----- ----- -------
Col_cuticle_N 1/1 11 42 .. 1 32 [. 7.1 1.1
B56 1/1 28 59 .. 381 412 .] 2.5 5.5
Collagen 1/3 110 138 .. 32 60 .] 20.8 0.00032
Collagen 2/3 155 213 .. 1 60 [] 34.8 4.4e-08
Collagen 3/3 225 284 .. 1 60 [] 29.2 1.5e-06
Alignments of top-scoring domains:
Col_cuticle_N: domain 1 of 1, from 11 to 42: score 7.1, E = 1.1
*->SgvAvlacLftvpsiyndInsfqdevmdemde<-*
S+++ l++L++v++ nd+++ + e+++e+ e
C39E9.3 11 SLFVFLSVLVFVLQTKNDLDQVWAEFDQEVQE 42
B56: domain 1 of 1, from 28 to 59: score 2.5, E = 5.5
*->EctaqYkeerqkekqreeeReelWkkLEelak<-*
++++ + e q+ +++ + Re+ W+ L +la
C39E9.3 28 DLDQVWAEFDQEVQEVTVLREASWNTLRNLAT 59
Collagen: domain 1 of 3, from 110 to 138: score 20.8, E = 0.00032
*->ppGepGpPGppGppGppGppGapGapGpp<-*
p+G++Gp G pG++G+pG+pG++G +G++
C39E9.3 110 PAGPSGPKGLPGQDGAPGEPGPAGKMGQN 138
Collagen: domain 2 of 3, from 155 to 213: score 34.8, E = 4.4e-08
*->GppGppGppGppGppGppGppGpaGapGppGppGepGpPGppGppGp
p+G++GppG+pG Gp+G+ G++G++G pG+ G+pG G Gp G+
C39E9.3 155 -PAGEMGPPGAPGKIGPRGQRGQSGGAGTPGNNGAPGHNGELGPCGQ 200
pGppGapGapGpp<-*
+GppG++Ga G +
C39E9.3 201 AGPPGPAGAIGRR 213
Collagen: domain 3 of 3, from 225 to 284: score 29.2, E = 1.5e-06
*->GppGppGppGppGppGppGppGpaGapGppGppGepGpPGppGppGp
Gp G pGp Gp G+ G++G G G Gp G G GpPG G G
C39E9.3 225 GPIGAPGPVGPVGMEGDRGNRGGLGVDGPLGSIGLQGPPGRTGSTGD 271
pGppGapGapGpp<-*
G+ G++G+ G+
C39E9.3 272 VGESGPIGPNGQD 284