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/F18A11.1
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Query: F18A11.1 CE09451 locus:puf-6 Pumilio-family RNA binding domains (aka PUM-HD, Pumilio homology domain) (6 domains) status:Partially_conf
Scores for sequence family classification (score includes all domains):
Model Description Score E-value N
-------- ----------- ----- ------- ---
PUF Pumilio-family RNA binding repeat 96.9 2.8e-26 6
AIRS AIR synthase related protein, N-terminal dom 7.8 0.7 1
Vps52 Vps52 / Sac2 family 4.1 2.3 1
Parsed for domains:
Model Domain seq-f seq-t hmm-f hmm-t score E-value
-------- ------- ----- ----- ----- ----- ----- -------
Vps52 1/1 118 134 .. 580 596 .] 4.1 2.3
PUF 1/6 128 163 .. 1 35 [] 17.9 0.002
AIRS 1/1 128 177 .. 1 56 [. 7.8 0.7
PUF 2/6 165 199 .. 1 35 [] 26.5 6.5e-06
PUF 3/6 249 274 .. 10 35 .] 17.5 0.0025
PUF 4/6 291 322 .. 5 35 .] 12.4 0.075
PUF 5/6 330 360 .. 5 35 .] 13.2 0.045
PUF 6/6 384 399 .. 12 27 .. 12.7 0.063
Alignments of top-scoring domains:
Vps52: domain 1 of 1, from 118 to 134: score 4.1, E = 2.3
*->eqetfqEllnsstenFv<-*
+ ++++E+l +st++Fv
F18A11.1 118 IRKAVFEKLTESTTLFV 134
PUF: domain 1 of 6, from 128 to 163: score 17.9, E = 0.002
*->sikgnlvqLstdqyGnyvlQkllevat.peqiqlil<-*
+ + +v L+ ++Gn+++Qkl e at+ eq++l+
F18A11.1 128 ESTTLFVGLCHSRNGNFIVQKLVELATpAEQRELLR 163
AIRS: domain 1 of 1, from 128 to 177: score 7.8, E = 0.7
*->dsltyksagvdgdagkslvslikelvkstfrpgvgsgtlvapGgdag
s t +++++++++g+++v+++ el +++ + + l+ ++ d+g
F18A11.1 128 ESTTLFVGLCHSRNGNFIVQKLVELATPAEQ-----RELLRQMIDGG 169
vfdlkdedp<-*
++ +++ d+
F18A11.1 170 LLVMCK-DK 177
PUF: domain 2 of 6, from 165 to 199: score 26.5, E = 6.5e-06
*->sikgnlvqLstdqyGnyvlQkllevatpeqiqlil<-*
i+g l+++++d+++++v+Q l++ + ++ ++++
F18A11.1 165 MIDGGLLVMCKDKFACRVVQLALQKFDHSNVFQLI 199
PUF: domain 3 of 6, from 249 to 274: score 17.5, E = 0.0025
*->stdqyGnyvlQkllevatpeqiqlil<-*
++d+yG++++Q+++++++++ + +++
F18A11.1 249 CQDKYGCRLVQQVIDRLAENPKLPCF 274
PUF: domain 4 of 6, from 291 to 322: score 12.4, E = 0.075
*->nlvqLstdqyGnyvlQkllevat.peqiqlil<-*
n++ Ls++ ++nyv+Q++++ + e +++++
F18A11.1 291 NCYRLSSNEFANYVIQYVIKSSGiMEMYRDTI 322
PUF: domain 5 of 6, from 330 to 360: score 13.2, E = 0.045
*->nlvqLstdqyGnyvlQkllevatpeqiqlil<-*
nl+++s+d+y+++v++ + +a+p ++ ++
F18A11.1 330 NLLSMSQDKYASHVIEGAFLFAPPALLHEMM 360
PUF: domain 6 of 6, from 384 to 399: score 12.7, E = 0.063
*->dqyGnyvlQkllevat<-*
+qyGnyv+Q+++ ++t
F18A11.1 384 HQYGNYVVQQMISICT 399