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).
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
HMM file: /home/niguts/usr02/tshini/ykclst/db/Pfam_fs
Sequence file: hmm4/seq/W04D2.6a
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Query: W04D2.6a CE32000 RNA recognition motif. (aka RRM, RBD, or RNP domain) status:Partially_confirmed TR:Q22859 protein_id:CAA99937.1
Scores for sequence family classification (score includes all domains):
Model Description Score E-value N
-------- ----------- ----- ------- ---
PWI PWI domain 147.0 4e-44 1
rrm RNA recognition motif. (a.k.a. RRM, RB 42.4 5e-11 1
Pencillinase_R Penicillinase repressor 4.2 6.3 1
Viral_P18 ssRNA positive strand viral 18kD cyste 4.2 8.1 1
Rota_VP2 Rotavirus VP2 protein 1.6 5.6 1
Parsed for domains:
Model Domain seq-f seq-t hmm-f hmm-t score E-value
-------- ------- ----- ----- ----- ----- ----- -------
rrm 1/1 49 119 .. 1 77 [] 42.4 5e-11
Rota_VP2 1/1 385 409 .. 1 25 [. 1.6 5.6
Pencillinase_R 1/1 407 421 .. 109 122 .] 4.2 6.3
Viral_P18 1/1 411 441 .. 100 131 .] 4.2 8.1
PWI 1/1 631 702 .. 1 84 [] 147.0 4e-44
Alignments of top-scoring domains:
rrm: domain 1 of 1, from 49 to 119: score 42.4, E = 5e-11
*->lfVgNLppdvteedLkdlFskfGpivsikivkDhiekpketgkskGf
+fVgN++ +++e ++++ ++G + s k +k +gk Gf
W04D2.6a 49 VFVGNISDKCSDEFIRKILNECGNVASWKRIKG------SNGKLQGF 89
aFVeFeseedAekAlealnGkelggrklrv<-*
+F+ F++ e+ +Al+ l+++ lg++kl+v
W04D2.6a 90 GFCHFTDLEGTLRALRILHEFHLGDKKLTV 119
Rota_VP2: domain 1 of 1, from 385 to 409: score 1.6, E = 5.6
*->MayRnrGakRrrntkkkDaekEket<-*
R+r R+r +kD+++E ++
W04D2.6a 385 FFQRKRDYEREREADQKDRMQEQQE 409
Pencillinase_R: domain 1 of 1, from 407 to 421: score 4.2, E = 6.3
*->geEIeEL.rdILnek<-*
+ EIeEL+r+I +e
W04D2.6a 407 QQEIEELkRQIMEEA 421
Viral_P18: domain 1 of 1, from 411 to 441: score 4.2, E = 8.1
*->eqLKtqiqvltaaaklekaavylpaklnrlkv<-*
e+LK qi + a ++++ +++ ++ k+ +lk+
W04D2.6a 411 EELKRQIMEEAANDESINIEE-EARKRHKLKE 441
PWI: domain 1 of 1, from 631 to 702: score 147.0, E = 4e-44
*->ldrIkPWItKrVteiLGfEDdtvvefIlsqiKqsKEKKDGEekknln
+drI+PW++K+Vt++LG+ED+++++fI++qi ek++++
W04D2.6a 631 NDRIRPWVAKKVTQFLGEEDKSFCDFICDQI----------EKQATP 667
skmLkiNltgfildeeAeeFVgkLWeLLIeeeksreg<-*
+++Lk+ +++i+de+Ae+FV+k+W+LLI+e+++r++
W04D2.6a 668 QEILKD--VAVIIDEDAEQFVIKMWRLLIYEGQARRL 702