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/C30F2.1
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Query: C30F2.1 CE17480 collagen status:Partially_confirmed TR:Q18327 protein_id:CAA94580.1
Scores for sequence family classification (score includes all domains):
Model Description Score E-value N
-------- ----------- ----- ------- ---
Collagen Collagen triple helix repeat (20 copies 60.2 4.6e-15 4
Col_cuticle_N Nematode cuticle collagen N-terminal do 7.6 0.78 1
Parsed for domains:
Model Domain seq-f seq-t hmm-f hmm-t score E-value
-------- ------- ----- ----- ----- ----- ----- -------
Col_cuticle_N 1/1 18 81 .. 1 66 [] 7.6 0.78
Collagen 1/4 110 133 .. 8 31 .. 10.6 0.19
Collagen 2/4 157 182 .. 35 60 .] 17.6 0.0023
Collagen 3/4 193 223 .. 30 60 .] 20.8 0.00032
Collagen 4/4 232 286 .. 1 55 [. 35.7 2.5e-08
Alignments of top-scoring domains:
Col_cuticle_N: domain 1 of 1, from 18 to 81: score 7.6, E = 0.78
*->SgvAvlacLftvpsiyndInsfqdevmdemdeFKvyaddaWneMvdv
S++A l+ +f+ +y++++ + +v + eF v ++ aW+++ ++
C30F2.1 18 SLIAALCGVFYYITVYQELSALSLNVKKSVAEFSVATNFAWEQIATL 64
qrnvrppskpasarfgrpf<-*
+ +++ + +++ f
C30F2.1 65 NELHLVSKRG--ISKKSVF 81
Collagen: domain 1 of 4, from 110 to 133: score 10.6, E = 0.19
*->ppGppGppGppGppGpaGapGppG<-*
ppGppGppG +G+pGp+G pG +G
C30F2.1 110 PPGPPGPPGCRGEPGPSGLPGRRG 133
Collagen: domain 2 of 4, from 157 to 182: score 17.6, E = 0.0023
*->epGpPGppGppGppGppGapGapGpp<-*
++GpPG +G++G G+pGapG G
C30F2.1 157 PRGPPGRRGRMGDDGEPGAPGRRGLS 182
Collagen: domain 3 of 4, from 193 to 223: score 20.8, E = 0.00032
*->pGppGepGpPGppGppGppGppGapGapGpp<-*
+GppGepG+PG pG pG pG++G++G G +
C30F2.1 193 RGPPGEPGEPGRPGTPGTPGNDGKDGRNGYR 223
Collagen: domain 4 of 4, from 232 to 286: score 35.7, E = 2.5e-08
*->GppGppGppGppGppGppGppGpaGapGppGppGepGpPGppGppGp
GppGp+G++G+pG +G pG G +G+ GppG +G++G+ G+pG pG
C30F2.1 232 GPPGPMGARGEPGHRGLPGDNGMPGPMGPPGYRGDNGRRGAPGLPGR 278
pGppGapG<-*
G G+pG
C30F2.1 279 TGRHGKPG 286