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: hmm1/seq/C09G5.5
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Query: C09G5.5 CE01485 collagen status:Partially_confirmed SW:Q09456 protein_id:CAA86758.1
Scores for sequence family classification (score includes all domains):
Model Description Score E-value N
-------- ----------- ----- ------- ---
Col_cuticle_N Nematode cuticle collagen N-terminal do 80.2 2e-22 1
Collagen Collagen triple helix repeat (20 copies 78.7 3.8e-20 3
Parsed for domains:
Model Domain seq-f seq-t hmm-f hmm-t score E-value
-------- ------- ----- ----- ----- ----- ----- -------
Col_cuticle_N 1/1 13 74 .. 1 66 [] 80.2 2e-22
Collagen 1/3 90 124 .. 26 60 .] 20.2 0.00047
Collagen 2/3 140 199 .. 1 60 [] 35.6 2.7e-08
Collagen 3/3 202 261 .. 1 60 [] 38.9 3.4e-09
Alignments of top-scoring domains:
Col_cuticle_N: domain 1 of 1, from 13 to 74: score 80.2, E = 2e-22
*->SgvAvlacLftvpsiyndInsfqdevmdemdeFKvyaddaWneMvdv
Sg++v+++L++v++iy+dInsf de+++e+++F+++a+daWn+Mv+
C09G5.5 13 SGIVVFGALISVFHIYTDINSFVDEAHRELGAFRGVANDAWNSMVNH 59
qrnvrppskpasarfgrpf<-*
+++r +a++ f+r+
C09G5.5 60 DDSAR----VARSVFVRRQ 74
Collagen: domain 1 of 3, from 90 to 124: score 20.2, E = 0.00047
*->apGppGppGepGpPGppGppGppGppGapGapGpp<-*
++GppGppG++G G +G+pGp+G pG+pG +Gp+
C09G5.5 90 PAGPPGPPGASGDRGLDGQPGPAGKPGQPGVAGPA 124
Collagen: domain 2 of 3, from 140 to 199: score 35.6, E = 2.7e-08
*->GppGppGppGppGppGppGppGpaGapGppGppGepGpPGppGppGp
Gp+G pG pGp+Gp G+pG+p + G++GppGppG++G G+pG++G+
C09G5.5 140 GPAGAPGNPGPQGPNGNPGAPAHGGGQGPPGPPGPAGDAGSPGQAGA 186
pGppGapGapGpp<-*
pG+pG+pG G++
C09G5.5 187 PGNPGRPGQSGQR 199
Collagen: domain 3 of 3, from 202 to 261: score 38.9, E = 3.4e-09
*->GppGppGppGppGppGppGppGpaGapGppGppGepGpPGppGppGp
G pGp G+pGp+GppG+pG+pG pGp+GppG+pGp G+pG+pG+
C09G5.5 202 GLPGPSGRPGPQGPPGAPGQPGSGSTPGPAGPPGPPGPNGQPGHPGQ 248
pGppGapGapGpp<-*
G+pGapG G+p
C09G5.5 249 DGQPGAPGNDGAP 261