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).
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
HMM file: /home/niguts/usr02/tshini/ykclst/db/Pfam_fs
Sequence file: hmm4/seq/PDB1.1
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
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