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: hmm2/seq/F08G5.4
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Query: F08G5.4 CE05574 collagen status:Partially_confirmed TR:Q19218 protein_id:CAA94581.1
Scores for sequence family classification (score includes all domains):
Model Description Score E-value N
-------- ----------- ----- ------- ---
Collagen Collagen triple helix repeat (20 copies 104.8 1.6e-27 3
Col_cuticle_N Nematode cuticle collagen N-terminal do 104.4 1.2e-29 1
Parsed for domains:
Model Domain seq-f seq-t hmm-f hmm-t score E-value
-------- ------- ----- ----- ----- ----- ----- -------
Col_cuticle_N 1/1 14 79 .. 1 66 [] 104.4 1.2e-29
Collagen 1/3 95 124 .. 1 31 [. 20.0 0.00051
Collagen 2/3 142 201 .. 1 60 [] 47.5 1.5e-11
Collagen 3/3 207 266 .. 1 60 [] 53.4 3.4e-13
Alignments of top-scoring domains:
Col_cuticle_N: domain 1 of 1, from 14 to 79: score 104.4, E = 1.2e-29
*->SgvAvlacLftvpsiyndInsfqdevmdemdeFKvyaddaWneMvdv
Sg+A++acLftv+ i+ dIn+++d+vmd+mdeFK++a++aW++M++v
F08G5.4 14 SGLAIVACLFTVGAIFKDINDLYDNVMDDMDEFKMFANNAWKDMIPV 60
qrnvrppskpasarfgrpf<-*
+r++ + + +a+fgr +
F08G5.4 61 TRPSLDNQSNLRAIFGREK 79
Collagen: domain 1 of 3, from 95 to 124: score 20.0, E = 0.00051
*->GppGppGppGppGppGppGppGpaGapGppG<-*
ppGppGppG+pG+pG+ G++G+aG+ G +G
F08G5.4 95 -PPGPPGPPGAPGAPGDDGHAGEAGKTGING 124
Collagen: domain 2 of 3, from 142 to 201: score 47.5, E = 1.5e-11
*->GppGppGppGppGppGppGppGpaGapGppGppGepGpPGppGppGp
G++Gp+Gp G+pG+pGp G+pG++G++G pG+pG++Gp G +G+pG
F08G5.4 142 GEAGPAGPDGAPGAPGPDGQPGQDGPAGQPGAPGPAGPEGDAGAPGD 188
pGppGapGapGpp<-*
+G pGapGapG+
F08G5.4 189 AGAPGAPGAPGQD 201
Collagen: domain 3 of 3, from 207 to 266: score 53.4, E = 3.4e-13
*->GppGppGppGppGppGppGppGpaGapGppGppGepGpPGppGppGp
G pG pG+pGp+Gp G+pG+ G+aGapG +Gp+G++Gp+G+pG++G+
F08G5.4 207 GLPGAPGAPGPQGPSGNPGQDGAAGAPGQAGPAGPAGPDGQPGQAGQ 253
pGppGapGapGpp<-*
G++G+ G +G+p
F08G5.4 254 DGEAGPEGNAGQP 266