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/W04D2.6a
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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



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