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: hmm5/seq/Y41D4A.2
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Query: Y41D4A.2 CE27619 status:Partially_confirmed TR:Q95Y22 protein_id:AAK68452.1
Scores for sequence family classification (score includes all domains):
Model Description Score E-value N
-------- ----------- ----- ------- ---
Collagen Collagen triple helix repeat (20 copies 98.2 1.6e-25 3
Col_cuticle_N Nematode cuticle collagen N-terminal do 44.9 6e-12 1
Peptidase_M50 Peptidase family M50 6.6 0.88 1
Parsed for domains:
Model Domain seq-f seq-t hmm-f hmm-t score E-value
-------- ------- ----- ----- ----- ----- ----- -------
Col_cuticle_N 1/1 21 81 .. 1 66 [] 44.9 6e-12
Collagen 1/3 106 137 .. 5 36 .. 15.9 0.007
Collagen 2/3 156 215 .. 1 60 [] 47.7 1.3e-11
Collagen 3/3 221 280 .. 1 60 [] 50.3 2.4e-12
Peptidase_M50 1/1 17 320 .. 101 132 .. 6.6 0.88
Alignments of top-scoring domains:
Col_cuticle_N: domain 1 of 1, from 21 to 81: score 44.9, E = 6e-12
*->SgvAvlacLftvpsiyndInsfqdevmdemdeFKvyaddaWneMvdv
S vAv+++ +t+p++yn++ + ++ e++++K+ a d+W+e+ +
Y41D4A.2 21 SVVAVISVSVTLPMVYNYVHHVKRSMQTEINFCKGSAKDIWTEVNHL 67
qrnvrppskpasarfgrpf<-*
+ + + ++r++r+
Y41D4A.2 68 KSIPAS-----RNRTARQA 81
Collagen: domain 1 of 3, from 106 to 137: score 15.9, E = 0.007
*->ppGppGppGppGppGppGpaGapGppGppGep<-*
+pG++Gp+G pG+pG pG aGapG pG+pG p
Y41D4A.2 106 LPGAAGPAGTPGKPGRPGKAGAPGLPGNPGRP 137
Collagen: domain 2 of 3, from 156 to 215: score 47.7, E = 1.3e-11
*->GppGppGppGppGppGppGppGpaGapGppGppGepGpPGppGppGp
Gp+GppGppGp+G +G G pG++G+ G pG++G++Gp Gp G pG+
Y41D4A.2 156 GPAGPPGPPGPAGDAGSDGSPGAPGSDGQPGAAGDKGPAGPNGNPGA 202
pGppGapGapGpp<-*
pG pG+pG+ G+
Y41D4A.2 203 PGSPGKPGEDGKS 215
Collagen: domain 3 of 3, from 221 to 280: score 50.3, E = 2.4e-12
*->GppGppGppGppGppGppGppGpaGapGppGppGepGpPGppGppGp
G+pGp+GppGp+GppG+pG+pG++G pG pGp+G++G PG+pG++G
Y41D4A.2 221 GAPGPAGPPGPQGPPGAPGQPGHDGQPGTPGPKGPNGNPGAPGADGN 267
pGppGapGapGpp<-*
pG pG +G +G
Y41D4A.2 268 PGTPGVAGVAGSG 280
Peptidase_M50: domain 1 of 1, from 17 to 320: score 6.6, E = 0.88
RF xxxxxxxxxxxxxxxxxx
*->iLAvvllalllllpgvvv.............................
++A+ + a+++++ ++ + ++ +++ ++ + ++++ ++ ++
Y41D4A.2 17 AVAFSVVAVISVSVTLPMvynyvhhvkrsmqteinfckgsakdiwte 63
RF
..................................................
++ ++ + +++++ ++ + + + +++++ ++ ++++ ++ ++ ++
Y41D4A.2 64 vnhlksipasrnrtarqagydagvngggseasgapgnceacclpgaagpa 113
RF
..................................................
+++++++++++ + ++ ++++++++++++ + ++++++++++++ +++++
Y41D4A.2 114 gtpgkpgrpgkagapglpgnpgrppqqpcepitpppckpcpqgpagppgp 163
RF
..................................................
+++ ++ +++++++ ++++++++ +++++ +++++++ ++++++++ ++
Y41D4A.2 164 pgpagdagsdgspgapgsdgqpgaagdkgpagpngnpgapgspgkpgedg 213
RF
..................................................
++ + +++ +++ ++++++++++ +++++++++++++++++++++++ ++
Y41D4A.2 214 ksepitpgapgpagppgpqgppgapgqpghdgqpgtpgpkgpngnpgapg 263
RF xxxxxxx
...........................................assglia
++++++++ + ++++ ++ +++ + +++ ++++++ ++++l++
Y41D4A.2 264 adgnpgtpgvagvagsggekgvcpkycaidggvffedgsrqsfFQTLLQS 313
RF xxxxxxx
llaflal<-*
la+ a+
Y41D4A.2 314 ALAYTAF 320