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/M195.1
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Query: M195.1 CE03514 cuticle collagen status:Partially_confirmed TR:Q21562 protein_id:CAA91290.1
Scores for sequence family classification (score includes all domains):
Model Description Score E-value N
-------- ----------- ----- ------- ---
Collagen Collagen triple helix repeat (20 copies 90.8 1.8e-23 3
Col_cuticle_N Nematode cuticle collagen N-terminal do 33.8 1.2e-08 1
Flavi_NS4A Flavivirus non-structural protein NS4A 3.0 4.4 1
Parsed for domains:
Model Domain seq-f seq-t hmm-f hmm-t score E-value
-------- ------- ----- ----- ----- ----- ----- -------
Flavi_NS4A 1/1 18 35 .. 132 149 .] 3.0 4.4
Col_cuticle_N 1/1 27 59 .. 1 33 [. 33.8 1.2e-08
Collagen 1/3 115 147 .. 28 60 .] 15.0 0.012
Collagen 2/3 163 222 .. 1 60 [] 48.2 9.3e-12
Collagen 3/3 230 289 .. 1 60 [] 43.9 1.4e-10
Alignments of top-scoring domains:
Flavi_NS4A: domain 1 of 1, from 18 to 35: score 3.0, E = 4.4
*->qLAyllIgilTlVgaVAA<-*
++A++ I+i T++ ++A
M195.1 18 KIAFFGICISTVATLTAI 35
Col_cuticle_N: domain 1 of 1, from 27 to 59: score 33.8, E = 1.2e-08
*->SgvAvlacLftvpsiyndInsfqdevmdemdeF<-*
S+vA l++++++ps+yn++++ q++++ e+d++
M195.1 27 STVATLTAIVAIPSLYNYMQTVQSTLQTEVDFC 59
Collagen: domain 1 of 3, from 115 to 147: score 15.0, E = 0.012
*->GppGppGepGpPGppGppGppGppGapGapGpp<-*
Gp+GppG pG++G +G +G+pGp+G+pG+ p+
M195.1 115 GPAGPPGTPGEDGRDGNDGQPGPDGQPGSDAPA 147
Collagen: domain 2 of 3, from 163 to 222: score 48.2, E = 9.3e-12
*->GppGppGppGppGppGppGppGpaGapGppGppGepGpPGppGppGp
GppGp+G +Gp G+pG++G+pG++G +G pG+pG +Gp+GppG++G+
M195.1 163 GPPGPAGNAGPKGAPGNAGAPGNDGQAGAPGAPGNDGPQGPPGQDGA 209
pGppGapGapGpp<-*
+G+pG++G pG +
M195.1 210 AGQPGPDGQPGVV 222
Collagen: domain 3 of 3, from 230 to 289: score 43.9, E = 1.4e-10
*->GppGppGppGppGppGppGppGpaGapGppGppGepGpPGppGppGp
GppGppGp G+pG +G pG +G++G Gp+Gp+G++G +G+pG++G+
M195.1 230 GPPGPPGPQGAPGTDGQPGSAGQPGQDGPQGPAGDAGTDGAPGQAGA 276
pGppGapGapGpp<-*
+G++G++G pG+
M195.1 277 AGEQGEAGQPGEG 289