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/PDB1.1
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Query:  PDB1.1  CE31209    status:Partially_confirmed TR:Q21611 protein_id:AAA81718.3

Scores for sequence family classification (score includes all domains):
Model         Description                               Score    E-value  N
--------      -----------                               -----    ------- ---
Cation_efflux Cation efflux family                      251.3    1.4e-71   1

Parsed for domains:
Model         Domain  seq-f seq-t    hmm-f hmm-t      score  E-value
--------      ------- ----- -----    ----- -----      -----  -------
Cation_efflux   1/1      62   338 ..     1   303 []   251.3  1.4e-71

Alignments of top-scoring domains:
Cation_efflux: domain 1 of 1, from 62 to 338: score 251.3, E = 1.4e-71
                   *->lwislalnlllavvKfiaGllsgSlALlaDavHslsDvaasliaLla
                      ++++++ln++l+++K i+ ++sgSlA+la+ v+s++D+++ +++++a
      PDB1.1    62    TTLTIILNVSLIIAKSIVAYFSGSLAILASVVDSFMDITSGVVVWYA 108

                   lriarkPaDrrhpfGhgRaEiLaalinavllfvvglggfilyeaierlls
                    ++ +k   +++p G +++E+L   i++++++++  ++++ +  ++++ +
      PDB1.1   109 CYKIEKMNKEQYPVGMRKLEPLTVVIVGMIMLFAN-FIVLERATVQTIED 157

                   PyeieedsShgdahepvdpglialivalislvvnlllalyllrggkktns
                                    dp+  + + +li l   +++ + l+ +++ ++s
      PDB1.1   158 ---------------KLDPR--VDLTTLIVLCTGTATKFCLFMICRVRKS 190

                   gnpalraaalHvlsDlLgSlgvlvgalliyftgngleWpwaDPiaallIs
                      a  ++a + ++D+L+++++l+ga++ + ++     ++aDP++a+ +s
      PDB1.1   191 --AACLVLAIDQRNDCLTNIVALLGAWIGQNWW-----KYADPLGAFMVS 233

                   llIlktafrllkesvniLldgvppeedle.kireiilsipgVkgvhdlrt
                    +I+ t+f +++e + +L++++++ e+++++    i+++ ++k+++ +++
      PDB1.1   234 GFIIVTWFLTIREHIPYLIGRRADQEFINrITNISINHDQRIKALDTVHV 283

                   wsiGpgefvlsvHievdpdlsleeaheiadeieerlleefpeiehvtihv
                   +++G++  v+ vH+++d+  +l+ ah++a++++ +l++++  +e++++h
      PDB1.1   284 YHFGEKFLVE-VHAVFDEPAPLQMAHDVAESLQVKLEKLPF-VERAFVHC 331

                   epeglee<-*
                   ++ ++++
      PDB1.1   332 DYKFDGD    338



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