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/D2089.4a
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Query: D2089.4a CE30508 locus:ptb-1 polypyrimidine tract binding protein status:Partially_confirmed TR:Q18999 protein_id:CAA85411.3
Scores for sequence family classification (score includes all domains):
Model Description Score E-value N
-------- ----------- ----- ------- ---
rrm RNA recognition motif. (a.k.a. RRM, RBD, o 93.9 3.6e-26 4
mRNA_cap_C mRNA capping enzyme, C-terminal domain 3.0 7.8 1
Parsed for domains:
Model Domain seq-f seq-t hmm-f hmm-t score E-value
-------- ------- ----- ----- ----- ----- ----- -------
rrm 1/4 123 190 .. 1 77 [] 31.2 1e-07
mRNA_cap_C 1/1 230 250 .. 139 159 .] 3.0 7.8
rrm 2/4 236 301 .. 3 77 .] 13.6 0.015
rrm 3/4 423 490 .. 1 77 [] 31.7 7.2e-08
rrm 4/4 540 608 .. 1 77 [] 17.4 0.0012
Alignments of top-scoring domains:
rrm: domain 1 of 4, from 123 to 190: score 31.2, E = 1e-07
*->lfVgNLppdvteedLkdlFskfGpivsikivkDhiekpketgkskGf
+ V+N+ppd + +L +l+ ++Gp+ + + k k +
D2089.4a 123 VHVRNIPPDLVDVELMQLCIQYGPVSNYMMLKG-----------KSQ 158
aFVeFeseedAekAlealnG..kelggrklrv<-*
aFVe+e+e +A++ ++ + +++++gr+l
D2089.4a 159 AFVEYEEEASAAAFVSGMTAvpIQIRGRTLFA 190
mRNA_cap_C: domain 1 of 1, from 230 to 250: score 3.0, E = 7.8
*->sTaekVlesIedpVtkEeLle<-*
s+++ ++e+++ pV++++L +
D2089.4a 230 SVLRTIIENMMFPVSLDVLYQ 250
rrm: domain 2 of 4, from 236 to 301: score 13.6, E = 0.015
*->VgNLppdvteedLkdlFskfGpivsikivkDhiekpketgkskGfaF
+ N + v+ + L++lF +G++ ++i++ +++++ +a
D2089.4a 236 IENMMFPVSLDVLYQLFTRYGKV--LRIIT-------FNKNNTFQAL 273
VeFeseedAekAlealnGkelggrklrv<-*
V++ + +A+ A++ l ++ +++ ++
D2089.4a 274 VQMSEANSAQLAKQGLENQNVYNGCCTL 301
rrm: domain 3 of 4, from 423 to 490: score 31.7, E = 7.2e-08
*->lfVgNL.ppdvteedLkdlFskfGpivsikivkDhiekpketgkskG
+ V+NL+ vt + L++lF+ +G+++++ki ++ k
D2089.4a 423 ILVSNLhEMKVTTDALFTLFGVYGDVMRVKILYN----------KKD 459
faFVeFeseedAekAlealnGkelggrklrv<-*
a +++ ++ +A+ Al l++ + +r +rv
D2089.4a 460 NALIQYSEPQQAQLALTHLDKVKWHDRLIRV 490
rrm: domain 4 of 4, from 540 to 608: score 17.4, E = 0.0012
*->lfVgNLppdvteedLkdlFskfGpi.vsikivkDhiekpketgkskG
l +N+p++v+ee+Lk++F++ G + +k ++ k
D2089.4a 540 LHLSNIPTSVSEEKLKEMFAEAGFAvKAFKFFP----------KDHK 576
faFVeFeseedAekAlealnG.kelggrklrv<-*
+a ++ e+ e A +Al a++++k ++ lrv
D2089.4a 577 MALCQLEDIETAIDALIAMHNhKLAENAHLRV 608