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:            hmm1/seq/B0399.1a
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Query:  B0399.1a  CE31869    status:Partially_confirmed TR:Q9XTJ3 protein_id:CAB03807.2

Scores for sequence family classification (score includes all domains):
Model      Description                                  Score    E-value  N
--------   -----------                                  -----    ------- ---
CaMBD      Calmodulin binding domain                    175.2    2.9e-50   1
SK_channel Calcium-activated SK potassium channel        62.5    2.8e-18   1
ion_trans  Ion transport protein                         15.0     0.0072   1

Parsed for domains:
Model      Domain  seq-f seq-t    hmm-f hmm-t      score  E-value
--------   ------- ----- -----    ----- -----      -----  -------
SK_channel   1/1     262   376 ..     1   111 [.    62.5  2.8e-18
ion_trans    1/1     439   542 ..   104   228 .]    15.0   0.0072
CaMBD        1/1     561   637 ..     1    82 []   175.2  2.9e-50

Alignments of top-scoring domains:
SK_channel: domain 1 of 1, from 262 to 376: score 62.5, E = 2.8e-18
                   *->kLGHRRALFEKRKRLsDYALiFGmFGivvmviEtEL.....sWGlYs
                      +   R+ LF +R ++ D  L   + G+  ++i+ EL+  ++s G+ +
    B0399.1a   262    RCRLRKQLFIRRNKVCDISLFLAVLGLLLVIIDSELtalssSTGI-T 307

                   KeslyslALKCLisLstiiLLGLvvlYHaREvqLFvvDnGADDWRiAmty
                   K+s  s+ L+    +st  L+  ++ YHa Ev++ ++D GADDWR+A
    B0399.1a   308 KDSPISIILRSACVVSTFFLICCLINYHAIEVKIALIDSGADDWRVAFST 357

                   ERvllisLEllvCAiHPvP<-*
                   +R + + +E+ vC i P P
    B0399.1a   358 DRFIKMLIEVCVCMICPFP    376

ion_trans: domain 1 of 1, from 439 to 542: score 15.0, E = 0.0072
                   *->llrrapglfefelrtlGWklqslgrslkslfnlllllllllfifaii
                      +l+r+ +       ++   ++  +++  +l  l++++l  +++ +++
    B0399.1a   439    ALNRISM-----DFRF---VIKTMMADHPLRVLIVFTLSYWMCMSWM 477

                   gvqlfggelnkccnpingntnFdnfgeaflwlFqtlTteGwgdimpdtla
                   + q   +         ++    + +++++++ ++t  ++G+gdi+p+
    B0399.1a   478 FTQCERYD--------GQLEVEHYYLNSMWFIMVTFMSIGYGDIVPN--- 516

                   gtvlgkiyfvifiilggflllNlfiavi<-*
                    t  g  + ++  i+g+  + + +ia+i
    B0399.1a   517 -TYCGRCLSITTGIVGA-GVSSALIAII    542

CaMBD: domain 1 of 1, from 561 to 637: score 175.2, E = 2.9e-50
                   *->DtqLTkelKnAAAnVLqETWRtVLlIyKhtklvskgdqgRlRkHQRK
                      D++LT+++KnAAA+VLqETW    +I+K++k+++kgd+ RlR+HQR+
    B0399.1a   561    DSKLTNQRKNAAASVLQETW----FIHKYKKALHKGDDLRLRHHQRR 603

                   FLkAIhakfRkVkwdqRklsEnaNslvDvaKtqsv<-*
                   FL++I+  fR++kwdqRkl+E++Nsl+Dv+K++s+
    B0399.1a   604 FLHSINE-FRRIKWDQRKLQEKGNSLLDVGKLHSD    637



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