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/C09G5.4
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Query: C09G5.4 CE01484 locus:col-39 collagen status:Partially_confirmed SW:Q09455 protein_id:CAA86757.1
Scores for sequence family classification (score includes all domains):
Model Description Score E-value N
-------- ----------- ----- ------- ---
Collagen Collagen triple helix repeat (20 copies 98.1 1.8e-25 3
Col_cuticle_N Nematode cuticle collagen N-terminal do 82.5 3.9e-23 1
Parsed for domains:
Model Domain seq-f seq-t hmm-f hmm-t score E-value
-------- ------- ----- ----- ----- ----- ----- -------
Col_cuticle_N 1/1 14 75 .. 1 66 [] 82.5 3.9e-23
Collagen 1/3 91 125 .. 26 60 .] 17.1 0.0033
Collagen 2/3 141 200 .. 1 60 [] 44.6 9.2e-11
Collagen 3/3 203 262 .. 1 60 [] 52.4 6.6e-13
Alignments of top-scoring domains:
Col_cuticle_N: domain 1 of 1, from 14 to 75: score 82.5, E = 3.9e-23
*->SgvAvlacLftvpsiyndInsfqdevmdemdeFKvyaddaWneMvdv
Sgv v+++Lf+v++iyndI+sf d++++e++eFK++a+daWn+Mv+
C09G5.4 14 SGVFVFGALFSVAQIYNDISSFADNAHRELGEFKGFANDAWNSMVNH 60
qrnvrppskpasarfgrpf<-*
+++r +a++ f+r++
C09G5.4 61 DDATR----VARSVFVRRH 75
Collagen: domain 1 of 3, from 91 to 125: score 17.1, E = 0.0033
*->apGppGppGepGpPGppGppGppGppGapGapGpp<-*
++GppGppG+pG G +G+pG +G+pG+pG +Gp
C09G5.4 91 PAGPPGPPGAPGDRGLDGQPGGAGNPGQPGVAGPK 125
Collagen: domain 2 of 3, from 141 to 200: score 44.6, E = 9.2e-11
*->GppGppGppGppGppGppGppGpaGapGppGppGepGpPGppGppGp
Gp+G pG+pGp+Gp G pG+pG+ G++Gp+Gp+G++G G+pG+ G+
C09G5.4 141 GPAGAPGAPGPQGPNGQPGHPGQGGSQGPAGPRGPAGDAGAPGQVGA 187
pGppGapGapGpp<-*
pG+pG++G G++
C09G5.4 188 PGNPGQAGRGGQR 200
Collagen: domain 3 of 3, from 203 to 262: score 52.4, E = 6.6e-13
*->GppGppGppGppGppGppGppGpaGapGppGppGepGpPGppGppGp
G pGp G+pGp+Gp G+pG+pG++G++G +Gp+G++Gp+G+pG+pG+
C09G5.4 203 GLPGPSGAPGPQGPSGAPGQPGQSGGQGQQGPAGPAGPDGQPGQPGQ 249
pGppGapGapGpp<-*
G++GapG G+p
C09G5.4 250 DGQAGAPGNDGAP 262