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: hmm4/seq/T13B5.4
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Query: T13B5.4 CE13609 cuticular collagen status:Partially_confirmed SW:P34804 protein_id:AAB71295.1
Scores for sequence family classification (score includes all domains):
Model Description Score E-value N
-------- ----------- ----- ------- ---
Collagen Collagen triple helix repeat (20 copies 72.7 1.7e-18 4
Col_cuticle_N Nematode cuticle collagen N-terminal do 34.7 6.6e-09 2
7tm_2 7 transmembrane receptor (Secretin fami 3.1 4.2 1
Parsed for domains:
Model Domain seq-f seq-t hmm-f hmm-t score E-value
-------- ------- ----- ----- ----- ----- ----- -------
7tm_2 1/1 10 35 .. 1 26 [. 3.1 4.2
Col_cuticle_N 1/2 24 56 .. 1 33 [. 33.1 2e-08
Col_cuticle_N 2/2 69 100 .. 30 66 .] 1.5 49
Collagen 1/4 130 162 .. 28 60 .] 17.6 0.0024
Collagen 2/4 178 237 .. 1 60 [] 43.2 2.1e-10
Collagen 3/4 241 268 .. 33 60 .] 15.1 0.012
Collagen 4/4 269 303 .. 26 60 .] 20.3 0.00043
Alignments of top-scoring domains:
7tm_2: domain 1 of 1, from 10 to 35: score 3.1, E = 4.2
*->allLkviytVGyslSsLvcLllaiai<-*
a++Lk + + G+s+S +++L+ ia+
T13B5.4 10 AESLKKLAFFGISVSTIATLTAIIAV 35
Col_cuticle_N: domain 1 of 2, from 24 to 56: score 33.1, E = 2e-08
*->SgvAvlacLftvpsiyndInsfqdevmdemdeF<-*
S++A l+++++vp++yn++++ q+ +++e+ F
T13B5.4 24 STIATLTAIIAVPMLYNYMQHVQSSLQNEVQYF 56
Col_cuticle_N: domain 2 of 2, from 69 to 100: score 1.5, E = 49
*->mdeFKvyaddaWneMvdvqrnvrppskpasarfgrpf<-*
++++K+++d W+e ++ ++ ++r +r+
T13B5.4 69 VEFCKHRTDGLWDEFHRFETVKGV-----DSRIKRDT 100
Collagen: domain 1 of 4, from 130 to 162: score 17.6, E = 0.0024
*->GppGppGepGpPGppGppGppGppGapGapGpp<-*
G +Gp+G+pG +G+pG++G +G+pG +G+ ++
T13B5.4 130 GAAGPAGAPGKDGAPGEDGKAGNPGTAGSDAEA 162
Collagen: domain 2 of 4, from 178 to 237: score 43.2, E = 2.1e-10
*->GppGppGppGppGppGppGppGpaGapGppGppGepGpPGppGppGp
Gp+Gp+G+pGp+GppGp+G+ G+ + G Gp+G+pGpPGp+G pG
T13B5.4 178 GPAGPAGGPGPAGPPGPAGADGNTPSGGGEGPAGPPGPPGPAGNPGT 224
pGppGapGapGpp<-*
G pG+pGapG++
T13B5.4 225 DGAPGNPGAPGQV 237
Collagen: domain 3 of 4, from 241 to 268: score 15.1, E = 0.012
*->pGepGpPGppGppGppGppGapGapGpp<-*
pG pGp G++GppGppGp+G+pG++G+
T13B5.4 241 PGTPGPAGAAGPPGPPGPAGNPGSAGAS 268
Collagen: domain 4 of 4, from 269 to 303: score 20.3, E = 0.00043
*->apGppGppGepGpPGppGppGppGppGapGapGpp<-*
+pGp+Gp+G++Gp+G+pG +G+pG pG++GapG
T13B5.4 269 EPGPAGPAGDAGPDGAPGNAGAPGAPGEAGAPGSG 303