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).
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
HMM file: /home/niguts/usr02/tshini/ykclst/db/Pfam_fs
Sequence file: hmm3/seq/K12D12.3
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Query: K12D12.3 CE02272 cuticle collagen status:Partially_confirmed TR:Q21437 protein_id:CAA88865.1
Scores for sequence family classification (score includes all domains):
Model Description Score E-value N
-------- ----------- ----- ------- ---
Collagen Collagen triple helix repeat (20 copies 76.6 1.4e-19 3
Col_cuticle_N Nematode cuticle collagen N-terminal do 69.1 3.9e-19 1
Parsed for domains:
Model Domain seq-f seq-t hmm-f hmm-t score E-value
-------- ------- ----- ----- ----- ----- ----- -------
Col_cuticle_N 1/1 14 73 .. 1 66 [] 69.1 3.9e-19
Collagen 1/3 128 153 .. 30 55 .. 12.5 0.058
Collagen 2/3 178 237 .. 1 60 [] 46.8 2.2e-11
Collagen 3/3 243 302 .. 1 60 [] 33.4 1.1e-07
Alignments of top-scoring domains:
Col_cuticle_N: domain 1 of 1, from 14 to 73: score 69.1, E = 3.9e-19
*->SgvAvlacLftvpsiyndInsfqdevmdemdeFKvyaddaWneMvdv
Sg+A+l++L+++++i+n ++++++e++ e+ +F++++d +W+++v++
K12D12.3 14 SGIALLCSLLALGQIFNNVQDYWTELDTEITSFRQETDAMWKDLVQI 60
qrnvrppskpasarfgrpf<-*
++n+ +r+gr+
K12D12.3 61 GTNAAT------NRRGRRD 73
Collagen: domain 1 of 3, from 128 to 153: score 12.5, E = 0.058
*->pGppGepGpPGppGppGppGppGapG<-*
+GppG++G+PG+pGp+G pG +G+pG
K12D12.3 128 AGPPGPKGSPGSPGPNGVPGVDGKPG 153
Collagen: domain 2 of 3, from 178 to 237: score 46.8, E = 2.2e-11
*->GppGppGppGppGppGppGppGpaGapGppGppGepGpPGppGppGp
G+pGp G+pG++G++G+ G G G G+pG+pGe G+PGp+G+ Gp
K12D12.3 178 GAPGPNGRPGLRGMKGADGGLGRTGHDGNPGHPGEMGAPGPQGKQGP 224
pGppGapGapGpp<-*
G +G++Ga G
K12D12.3 225 DGRQGEKGADGRK 237
Collagen: domain 3 of 3, from 243 to 302: score 33.4, E = 1.1e-07
*->GppGppGppGppGppGppGppGpaGapGppGppGepGpPGppGppGp
Gp+G++Gp G++Gp G+ G Gp G++Gp+Gp+G +G PG +G +G
K12D12.3 243 GPKGQRGPQGEQGPVGDNGRNGPVGGAGPAGPQGGSGGPGEKGLDGG 289
pGppGapGapGpp<-*
pG +G+ G pG+
K12D12.3 290 PGSEGKVGRPGKD 302