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/R13F6.6
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Query:  R13F6.6  CE31722  locus:zak-1  status:Partially_confirmed TR:Q21982 protein_id:AAC47047.4

Scores for sequence family classification (score includes all domains):
Model          Description                              Score    E-value  N
--------       -----------                              -----    ------- ---
pkinase        Protein kinase domain                     65.5    4.5e-17   1
SAM            SAM domain (Sterile alpha motif)          11.2       0.12   1
Cauli_DNA-bind Caulimovirus DNA-binding protein           3.0        7.5   1
CPSase_L_D3    Carbamoyl-phosphate synthetase large c     2.6        2.2   1

Parsed for domains:
Model          Domain  seq-f seq-t    hmm-f hmm-t      score  E-value
--------       ------- ----- -----    ----- -----      -----  -------
pkinase          1/1       2    81 ..   172   288 ..    65.5  4.5e-17
Cauli_DNA-bind   1/1      78    98 ..     1    21 [.     3.0      7.5
SAM              1/1     170   207 ..    30    68 .]    11.2     0.12
CPSase_L_D3      1/1     439   449 ..     1    11 [.     2.6      2.2

Alignments of top-scoring domains:
pkinase: domain 1 of 1, from 2 to 81: score 65.5, E = 4.5e-17
                   *->vilegrgysskvDvWSlGviLyElltggplfpgadlpaftggdevdq
                      + l++ g +++ DvWS+Gv+L+E+l++
     R13F6.6     2    I-LQSEGLTTATDVWSYGVVLWEILSK-------------------- 27

                   liifvlklPfsdelpktridpleelfriikrpglrlplpsncSeelkdLl
                         + P++d       + ++    i++  g +l +p++c+ +lk+L+
     R13F6.6    28 ------EVPYKD------YSEFRIFTMITQS-GITLAIPPSCPAPLKQLM 64

                   kkcLnkDPskRpGsatakei<-*
                   + c+++ P++R    ++++i
     R13F6.6    65 SNCWKMTPKDRA---NMRQI    81

Cauli_DNA-bind: domain 1 of 1, from 78 to 98: score 3.0, E = 7.5
                   *->LaailsEieevlsdqkkikae<-*
                      + +i+ E   +  +qkk+  +
     R13F6.6    78    MRQIQGELNRLAGNQKKMRKD    98

SAM: domain 1 of 1, from 170 to 207: score 11.2, E = 0.12
                   *->nsidgvalltlteeDLkdiGgvtllGHrkkIlssIqgLk<-*
                      n i g  ll +t++DL+ +G v ++G r  +++ I++L
     R13F6.6   170    NRITGARLLGMTQNDLEHLG-VHKVGSRIELMKMIRKLA    207

CPSase_L_D3: domain 1 of 1, from 439 to 449: score 2.6, E = 2.2
                   *->lreeLrtPtdd<-*
                      l+e+LrtP++d
     R13F6.6   439    LQEQLRTPSPD    449



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