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/F20C5.1
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Query:  F20C5.1  CE03238  locus:pme-3  status:Partially_confirmed TR:Q19637 protein_id:CAA92299.1

Scores for sequence family classification (score includes all domains):
Model          Description                              Score    E-value  N
--------       -----------                              -----    ------- ---
PARG           Poly (ADP-ribose) glycohydrolase (PARG   792.0   1.1e-239   1
PsbJ           PsbJ                                       7.9       0.65   1
F-protein      Negative factor, (F-Protein) or Nef        6.4        0.6   1
Ran_BP1        RanBP1 domain                              5.3          3   1
Phage_portal_2 Phage portal protein, lambda family        2.9        6.6   1

Parsed for domains:
Model          Domain  seq-f seq-t    hmm-f hmm-t      score  E-value
--------       ------- ----- -----    ----- -----      -----  -------
F-protein        1/1     353   376 ..   217   240 .]     6.4      0.6
PsbJ             1/1     543   581 ..     1    39 []     7.9     0.65
Phage_portal_2   1/1     592   607 ..   369   384 .]     2.9      6.6
PARG             1/1     356   704 ..     1   420 []   792.0 1.1e-239
Ran_BP1          1/1     694   713 ..   108   127 .]     5.3        3

Alignments of top-scoring domains:
F-protein: domain 1 of 1, from 353 to 376: score 6.4, E = 0.6
                   *->vWkFDstLAyeYkAfelyPeefkd<-*
                      +W+FD+   y+  A e+y +e+ +
     F20C5.1   353    MWEFDPDITYKLPALEMYYKEMSE    376

PsbJ: domain 1 of 1, from 543 to 581: score 7.9, E = 0.65
                   *->mantgRiPLWlvgtvaGlaaigvlglFfYGsysglgssl<-*
                      m  +  + + l   ++ l ai+++g +++ sy+g g  l
     F20C5.1   543    MCPEMMVGMLLCEKMKQLEAISIVGAYVFSSYTGYGHTL    581

Phage_portal_2: domain 1 of 1, from 592 to 607: score 2.9, E = 6.6
                   *->RaglvEsrrrfmilqk<-*
                      R+ ++E+r+rf  l+
     F20C5.1   592    RQNTNEFRDRFGRLRV    607

PARG: domain 1 of 1, from 356 to 704: score 792.0, E = 1.1e-239
                   *->fDEeleaeaellLkfpslleseivnadellekiktgvRlLksakngi
                      fD++++ +++++L+++++++se+v+++e+lek+++++R++k+a++++
     F20C5.1   356    FDPDIT-YKLPALEMYYKEMSELVGREEVLEKFARVARIAKTAEDIL 401

                   velSQeLIGaLLaaaFfClFPrdnrakmkleysnfPdlsFnrlyqsrssa
                   +e++++L+G++++a+++++++++++a+m+++++++P +sF+r+++s++s+
     F20C5.1   402 PERIYRLVGDVESATLSHKQCAALVARMFFARPDSP-FSFCRILSSDKSI 450

                   qvEKLKclfhYFrRvsPtERDAsdvPtGaVSFeRkslekeqDSStLdeee
                   +vEKLK+lf+YF+++s      +d+P+GaVSF++++++k++     ++ee
     F20C5.1   451 CVEKLKFLFTYFDKMS------MDPPDGAVSFRLTKMDKDT-----FNEE 489

                   WsksdvnllPlhvtfegtiedegagaLQVDFANKyLGGGVLghGAvcVQE
                   W+++++++lP++++f++++++++a+++QVDFAN++LGGGVL+hG  +VQE
     F20C5.1   490 WKDKKLRSLPEVEFFDEMLIEDTALCTQVDFANEHLGGGVLNHG--SVQE 537

                   EIRFmInPELiVGmLFlevmddlEAIeIVGAErFSsYTGYASSFRFAGEY
                   EIRF+++PE++VGmL++e+m++lEAI+IVGA++FSsYTG
     F20C5.1   538 EIRFLMCPEMMVGMLLCEKMKQLEAISIVGAYVFSSYTG----------- 576

                   iDKKAmDpYaktlkWavaiddlsepnvneFkDesgRREiNKALCGFLNCS
                           Y++tlkWa++++++s++n+neF+D++gR
     F20C5.1   577 --------YGHTLKWAELQPNHSRQNTNEFRDRFGR-------------- 604

                   KAWEHqNiFmDEGDsvlqteivAIDAllfrgsllqcrreqLndekleREl
                                   l++e++AIDA+lf+gs+l+c++eqLn+++++RE+
     F20C5.1   605 ----------------LRVETIAIDAILFKGSKLDCQTEQLNKANIIREM 638

                   nkAsigFlslgvgpsnlpAvvtGnwGCGNWGCGAFgGDkpLKalIQllAa
                   +kAsigF+s+g++++n+p +vtG+wGCG     AF+GDkpLK++IQ++Aa
     F20C5.1   639 KKASIGFMSQGPKFTNIP-IVTGWWGCG-----AFNGDKPLKFIIQVIAA 682

                   aqadRPlvSYyTFGdeELrndcq<-*
                   ++adRPl+ +++FG++EL+++c+
     F20C5.1   683 GVADRPLH-FCSFGEPELAAKCK    704

Ran_BP1: domain 1 of 1, from 694 to 713: score 5.3, E = 3
                   *->FKtkEeAdeFKkkFEeaqke<-*
                      F+ +E A++ Kk++E  +++
     F20C5.1   694    FGEPELAAKCKKIIERMKQK    713



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