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/K02D7.3
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Query: K02D7.3 CE17996 cuticular collagen status:Partially_confirmed TR:O45105 protein_id:AAC02608.1
Scores for sequence family classification (score includes all domains):
Model Description Score E-value N
-------- ----------- ----- ------- ---
Collagen Collagen triple helix repeat (20 copies 67.9 3.5e-17 4
Col_cuticle_N Nematode cuticle collagen N-terminal do 40.9 9.8e-11 1
Parsed for domains:
Model Domain seq-f seq-t hmm-f hmm-t score E-value
-------- ------- ----- ----- ----- ----- ----- -------
Col_cuticle_N 1/1 27 69 .. 1 43 [. 40.9 9.8e-11
Collagen 1/4 126 158 .. 28 60 .] 17.8 0.0021
Collagen 2/4 174 233 .. 1 60 [] 42.7 3e-10
Collagen 3/4 237 264 .. 18 45 .. 12.9 0.048
Collagen 4/4 265 302 .. 23 60 .] 17.8 0.0021
Alignments of top-scoring domains:
Col_cuticle_N: domain 1 of 1, from 27 to 69: score 40.9, E = 9.8e-11
*->SgvAvlacLftvpsiyndInsfqdevmdemdeFKvyaddaWne<-*
S++A l ++++vp++yn+I++ q+ ++ e++++ ++++ W+e
K02D7.3 27 STIATLIAIVAVPMLYNYIQHVQSSLQSEVEFCAHRSNGLWDE 69
Collagen: domain 1 of 4, from 126 to 158: score 17.8, E = 0.0021
*->GppGppGepGpPGppGppGppGppGapGapGpp<-*
G++Gp+G pG++G+pG +G+pG pG+pG +
K02D7.3 126 GSAGPAGSPGQDGAPGNDGAPGAPGNPGQDAQD 158
Collagen: domain 2 of 4, from 174 to 233: score 42.7, E = 3e-10
*->GppGppGppGppGppGppGppGpaGapGppGppGepGpPGppGppGp
GppGp G+pG Gp G+pG+pG +G++ pGppG++GpPGp G+pG+
K02D7.3 174 GPPGPSGAPGQKGPSGAPGQPGRSGGASLPGPPGPAGPPGPSGQPGS 220
pGppGapGapGpp<-*
G++GapGapG +
K02D7.3 221 NGNAGAPGAPGHV 233
Collagen: domain 3 of 4, from 237 to 264: score 12.9, E = 0.048
*->pGppGpaGapGppGppGepGpPGppGpp<-*
pG pGpaG+pGp+Gp+G+pG+PG++G++
K02D7.3 237 PGTPGPAGPPGPAGPAGAPGQPGQAGHA 264
Collagen: domain 4 of 4, from 265 to 302: score 17.8, E = 0.0021
*->paGapGppGppGepGpPGppGppGppGppGapGapGpp<-*
++G pGp+G++G+pG+PG+pG +G+pG++G +G G++
K02D7.3 265 QPGQPGPQGDAGAPGAPGQPGSAGQPGNDGGDGGQGAC 302