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/C34F6.2
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Query: C34F6.2 CE15671 collagen status:Confirmed TR:O17641 protein_id:CAB03941.1
Scores for sequence family classification (score includes all domains):
Model Description Score E-value N
-------- ----------- ----- ------- ---
Collagen Collagen triple helix repeat (20 copies 65.0 2.3e-16 4
Col_cuticle_N Nematode cuticle collagen N-terminal do 13.3 0.016 1
Adenyl_transf Streptomycin adenylyltransferase 2.2 6.1 1
Parsed for domains:
Model Domain seq-f seq-t hmm-f hmm-t score E-value
-------- ------- ----- ----- ----- ----- ----- -------
Col_cuticle_N 1/1 24 57 .. 1 34 [. 13.3 0.016
Adenyl_transf 1/1 63 73 .. 1 11 [. 2.2 6.1
Collagen 1/4 96 121 .. 1 26 [. 16.2 0.0056
Collagen 2/4 142 201 .. 1 60 [] 26.6 8.1e-06
Collagen 3/4 207 259 .. 8 60 .] 42.4 3.7e-10
Collagen 4/4 260 271 .. 49 60 .] 2.2 40
Alignments of top-scoring domains:
Col_cuticle_N: domain 1 of 1, from 24 to 57: score 13.3, E = 0.016
*->SgvAvlacLftvpsiyndInsfqdevmdemdeFK<-*
S+vA l ++++vp + +++ ++ + de+ ++K
C34F6.2 24 STVATLIAIIAVPLLCLHMQTVHSGLSDELLFCK 57
Adenyl_transf: domain 1 of 1, from 63 to 73: score 2.2, E = 6.1
*->MRtEkEmLDvv<-*
MR+E E+L v+
C34F6.2 63 MRSEIEKLSVI 73
Collagen: domain 1 of 4, from 96 to 121: score 16.2, E = 0.0056
*->GppGppGppGppGppGppGppGpaGa<-*
Gp+G pG G+pG +G++G+pG++Ga
C34F6.2 96 GPAGVPGQEGAPGNDGKAGQPGAPGA 121
Collagen: domain 2 of 4, from 142 to 201: score 26.6, E = 8.1e-06
*->GppGppGppGppGppGppGppGpaGapGppGppGepGpPGppGppGp
GppG G+pGp GppGppG pG+ G+pG G++G+pGp GppG++Gp
C34F6.2 142 GPPGAVGGPGPKGPPGPPGGPGELGGPGRGGNRGPPGPRGPPGEAGP 188
pGppGapGapGpp<-*
G+ G+pG +G+
C34F6.2 189 DGEGGRPGQAGQT 201
Collagen: domain 3 of 4, from 207 to 259: score 42.4, E = 3.7e-10
*->ppGppGppGppGppGpaGapGppGppGepGpPGppGppGppGppGap
ppG pG+pG+pG pG++G+ G +G+pG +GpPGppG +G +G+pG++
C34F6.2 207 PPGQPGQPGEPGSPGEPGPDGRAGHPGRNGPPGPPGDNGGQGEPGKD 253
GapGpp<-*
G+ G++
C34F6.2 254 GEDGEN 259
Collagen: domain 4 of 4, from 260 to 271: score 2.2, E = 40
*->GppGapGapGpp<-*
G +Ga+G++G +
C34F6.2 260 GAAGAAGPKGSC 271