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/T28C6.6
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Query: T28C6.6 CE03749 locus:col-3 cuticle collagen status:Partially_confirmed TR:Q27318 protein_id:CAA90997.1
Scores for sequence family classification (score includes all domains):
Model Description Score E-value N
-------- ----------- ----- ------- ---
Collagen Collagen triple helix repeat (20 copies 86.7 2.4e-22 3
Col_cuticle_N Nematode cuticle collagen N-terminal do 46.3 2.3e-12 1
Parsed for domains:
Model Domain seq-f seq-t hmm-f hmm-t score E-value
-------- ------- ----- ----- ----- ----- ----- -------
Col_cuticle_N 1/1 21 80 .. 1 66 [] 46.3 2.3e-12
Collagen 1/3 102 135 .. 27 60 .] 11.6 0.11
Collagen 2/3 149 207 .. 1 60 [] 40.6 1.1e-09
Collagen 3/3 216 275 .. 1 60 [] 51.2 1.4e-12
Alignments of top-scoring domains:
Col_cuticle_N: domain 1 of 1, from 21 to 80: score 46.3, E = 2.3e-12
*->SgvAvlacLftvpsiyndInsfqdevmdemdeFKvyaddaWneMvdv
S vAv+++++t+p++yn++ + +++ e++++K+ a d+W e+ +
T28C6.6 21 SVVAVISVCVTLPMVYNYVHHVKRTMHSEINFCKGSAKDIWSEVNHL 67
qrnvrppskpasarfgrpf<-*
+ +++ +r++r+
T28C6.6 68 KAIPSG------NRTARQA 80
Collagen: domain 1 of 3, from 102 to 135: score 11.6, E = 0.11
*->pGppGppGepGpPGppGppGppGppGapGapGpp<-*
pG +Gp+G pG PG pG+pG+pG pG+pG p +
T28C6.6 102 PGAAGPAGTPGKPGRPGKPGAPGLPGNPGRPPQQ 135
Collagen: domain 2 of 3, from 149 to 207: score 40.6, E = 1.1e-09
*->GppGppGppGppGppGppGppGpaGapGppGppGepGpPGppGppGp
p+Gp+G+pGp+Gp+G++G+ G++GapG+ G pG+pG Gp Gp+G
T28C6.6 149 -PAGPAGAPGPAGPAGDAGANGNPGAPGNDGQPGAPGNKGPSGPNGN 194
pGppGapGapGpp<-*
pG pGapG pG+
T28C6.6 195 PGAPGAPGQPGQD 207
Collagen: domain 3 of 3, from 216 to 275: score 51.2, E = 1.4e-12
*->GppGppGppGppGppGppGppGpaGapGppGppGepGpPGppGppGp
G+pGp+Gp+Gp+GppG+pG+pG++G pG pGp+G++G PG+pG++G
T28C6.6 216 GAPGPAGPAGPQGPPGAPGQPGHDGQPGAPGPKGPNGNPGAPGADGN 262
pGppGapGapGpp<-*
pG pG++G G +
T28C6.6 263 PGAPGQAGTSGGA 275