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: hmm4/seq/T10B10.1
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Query: T10B10.1 CE06399 locus:col-41 collagen status:Partially_confirmed TR:Q22369 protein_id:CAA96674.1
Scores for sequence family classification (score includes all domains):
Model Description Score E-value N
-------- ----------- ----- ------- ---
Collagen Collagen triple helix repeat (20 copies 84.8 8.2e-22 3
Col_cuticle_N Nematode cuticle collagen N-terminal do 70.3 1.7e-19 1
HAMP HAMP domain 4.8 9.6 1
Parsed for domains:
Model Domain seq-f seq-t hmm-f hmm-t score E-value
-------- ------- ----- ----- ----- ----- ----- -------
HAMP 1/1 4 38 .. 1 35 [. 4.8 9.6
Col_cuticle_N 1/1 12 76 .. 1 66 [] 70.3 1.7e-19
Collagen 1/3 94 123 .. 14 43 .. 10.9 0.16
Collagen 2/3 142 201 .. 1 60 [] 45.5 5.2e-11
Collagen 3/3 208 267 .. 1 60 [] 44.0 1.3e-10
Alignments of top-scoring domains:
HAMP: domain 1 of 1, from 4 to 38: score 4.8, E = 9.6
*->lllvlllalllalllalllarrltrPlrrLaeaaq<-*
l+ ++++++ll+++ al + +++ +++L++ ++
T10B10.1 4 LGYIGAGVCLLGVFSALCSIGHIVQDINNLRSEVE 38
Col_cuticle_N: domain 1 of 1, from 12 to 76: score 70.3, E = 1.7e-19
*->SgvAvlacLftvpsiyndInsfqdevmdemdeFKvyaddaWneMvdv
+++ v+++L+++++i++dIn++++ev++ +deFKv+add+W++++ +
T10B10.1 12 CLLGVFSALCSIGHIVQDINNLRSEVEGRVDEFKVLADDTWDRLLIL 58
qrnvrppskpasarfgrpf<-*
q++++++ +p + + r++
T10B10.1 59 QSPTGESANP-VPSLLRNK 76
Collagen: domain 1 of 3, from 94 to 123: score 10.9, E = 0.16
*->ppGppGppGpaGapGppGppGepGpPGppG<-*
p+G+pGppG++G++G+ G+pG+ G+ G+ G
T10B10.1 94 PAGAPGPPGNPGKRGDEGHPGDEGRRGASG 123
Collagen: domain 2 of 3, from 142 to 201: score 45.5, E = 5.2e-11
*->GppGppGppGppGppGppGppGpaGapGppGppGepGpPGppGppGp
Gp+GppGp G+ Gp G pG +G++G+ G+ G+pG G+PG +G+ Gp
T10B10.1 142 GPAGPPGPDGDSGPEGFPGLQGQSGPSGEDGAPGQEGAPGDQGEQGP 188
pGppGapGapGpp<-*
+G +G +G+ G+p
T10B10.1 189 KGYDGTDGPDGQP 201
Collagen: domain 3 of 3, from 208 to 267: score 44.0, E = 1.3e-10
*->GppGppGppGppGppGppGppGpaGapGppGppGepGpPGppGppGp
G +G+pG+pG G+pG pG+ G++G+ G+ Gp+G+pG PG +G++ +
T10B10.1 208 GQAGQPGEPGWLGEPGLPGQHGEPGKDGEEGPQGAPGTPGNAGHDAF 254
pGppGapGapGpp<-*
pG pG++G pG+p
T10B10.1 255 PGTPGQAGKPGAP 267