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: hmm4/seq/M110.1
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Query: M110.1 CE02274 collagen status:Partially_confirmed TR:Q21528 protein_id:CAA90258.1
Scores for sequence family classification (score includes all domains):
Model Description Score E-value N
-------- ----------- ----- ------- ---
Collagen Collagen triple helix repeat (20 copi 88.7 6.9e-23 4
Col_cuticle_N Nematode cuticle collagen N-terminal 15.8 0.0028 1
AgrB Accessory gene regulator B 3.1 7.3 1
Na_H_antiporter Na+/H+ antiporter family 3.1 9.6 1
Parsed for domains:
Model Domain seq-f seq-t hmm-f hmm-t score E-value
-------- ------- ----- ----- ----- ----- ----- -------
Na_H_antiporter 1/1 27 55 .. 290 319 .] 3.1 9.6
AgrB 1/1 45 56 .. 176 187 .] 3.1 7.3
Col_cuticle_N 1/1 37 95 .. 1 66 [] 15.8 0.0028
Collagen 1/4 108 141 .. 27 60 .] 17.5 0.0025
Collagen 2/4 159 184 .. 35 60 .] 19.1 0.00093
Collagen 3/4 185 215 .. 1 31 [. 20.3 0.00044
Collagen 4/4 227 286 .. 1 60 [] 54.9 1.3e-13
Alignments of top-scoring domains:
Na_H_antiporter: domain 1 of 1, from 27 to 55: score 3.1, E = 9.6
*->GgvdHisytpfpyflfyapilaiplgvfGl<-*
+ + ++s t++ +f f+a i+++pl ++ +
M110.1 27 QSILVVS-TVISTFTFLATITLLPLFYMKV 55
AgrB: domain 1 of 1, from 45 to 56: score 3.1, E = 7.3
*->ItLLPIffsked<-*
ItLLP f+ k
M110.1 45 ITLLPLFYMKVQ 56
Col_cuticle_N: domain 1 of 1, from 37 to 95: score 15.8, E = 0.0028
*->SgvAvlacLftvpsiyndInsfqdevmdemdeFKvyaddaWneMvdv
S++ la+++ +p y +++ ++++++ +++++ + + d+W+++ +
M110.1 37 STFTFLATITLLPLFYMKVQRINSQMLTDLRNCHQDSTDIWKQLSQE 83
qrnvrppskpasarfgrpf<-*
++ + + +gr+
M110.1 84 NVRGKRS-------YGRDA 95
Collagen: domain 1 of 4, from 108 to 141: score 17.5, E = 0.0025
*->pGppGppGepGpPGppGppGppGppGapGapGpp<-*
+G pGp G++Gp+G pG+pG G G+ G G+
M110.1 108 QGKPGPTGPKGPDGGPGQPGLIGLNGRNGRNGKY 141
Collagen: domain 2 of 4, from 159 to 184: score 19.1, E = 0.00093
*->epGpPGppGppGppGppGapGapGpp<-*
+pGpPG+pG+ Gp+G +G++G +G++
M110.1 159 PPGPPGHPGRKGPRGTAGNAGTAGKN 184
Collagen: domain 3 of 4, from 185 to 215: score 20.3, E = 0.00044
*->GppGppGppGppGppGppGppGpaGapGppG<-*
G pG++GppGp+G +GppG+ G +G++G+pG
M110.1 185 GIPGRMGPPGPAGVRGPPGELGMRGPQGDPG 215
Collagen: domain 4 of 4, from 227 to 286: score 54.9, E = 1.3e-13
*->GppGppGppGppGppGppGppGpaGapGppGppGepGpPGppGppGp
G+pG+ G++G +G +G+ G pG G pG +G +Ge+G+ G++GppGp
M110.1 227 GRPGKVGSRGKAGHTGRDGRPGLEGTPGTRGVQGERGSRGARGPPGP 273
pGppGapGapGpp<-*
pGp+G +G +G +
M110.1 274 PGPAGSDGRKGSC 286