Protein Info for GFF3508 in Variovorax sp. SCN45

Annotation: Multidrug efflux system, outer membrane factor lipoprotein => OpmD of MexHI-OpmD system

These analyses and tools can help you predict a protein's function, but be skeptical. For enzymes, over 10% of annotations from KEGG or SEED are probably incorrect. For other types of proteins, the error rates may be much higher. MetaCyc and Swiss-Prot have low error rates, but the best hits in these databases are often quite distant, so this protein's function may not be the same. TIGRFam has low error rates. Finally, many experimentally-characterized proteins are not in any of these databases. To find relevant papers, use PaperBLAST.

Protein Families and Features

1 50 100 150 200 250 300 350 400 450 477 signal peptide" amino acids 1 to 22 (22 residues), see Phobius details TIGR01845: efflux transporter, outer membrane factor (OMF) lipoprotein, NodT family" amino acids 13 to 464 (452 residues), 334 bits, see alignment E=7.6e-104 PF02321: OEP" amino acids 63 to 251 (189 residues), 74.4 bits, see alignment E=5.5e-25 amino acids 283 to 462 (180 residues), 79.5 bits, see alignment E=1.4e-26

Best Hits

KEGG orthology group: None (inferred from 90% identity to vpe:Varpa_5699)

Predicted SEED Role

"RND efflux system, outer membrane lipoprotein CmeC" in subsystem Multidrug Resistance Efflux Pumps or Multidrug efflux pump in Campylobacter jejuni (CmeABC operon)

Sequence Analysis Tools

PaperBLAST (search for papers about homologs of this protein)

Search CDD (the Conserved Domains Database, which includes COG and superfam)

Search structures

Predict protein localization: PSORTb (Gram-negative bacteria)

Predict transmembrane helices and signal peptides: Phobius

Check the current SEED with FIGfam search

Find homologs in fast.genomics or the ENIGMA genome browser

Find the best match in UniProt

Protein Sequence (477 amino acids)

>GFF3508 Multidrug efflux system, outer membrane factor lipoprotein => OpmD of MexHI-OpmD system (Variovorax sp. SCN45)
MSRLFSYAAPFALSLLVLAGCAVGPKYTAPSDAPVAISAPERSLFAGDAVQRDWWRQLDD
PQLDALIDRALAENHEIRIAQARLLEARATQTEAELDRLPVVTASASKTRGIAQGNDGLQ
PDVRSLSQSSRAGFDASWEIDLFGRLKRLDEAATARAEASAADLEQVRIVAVAELARNYY
EMRGAEQRIAVTRRTLDSLRQSLRVTEAQVRTGRGLEGDLASAQANLATTESQLPALETA
RRQSAYRVAVLAGLRPAELEPMLRPQPLRVLDKRLPIGDMADLLRRRPDVLRAERGLAAS
TADVGAVTAELYPRFDIGGFLGFIALRGSDLGSSSSRAFSVTPGVSWPALRLGSVKARVR
GAEARAQGDRALYEQTVLRAIEDVEGALTGYGQNQLRLQRLVEASARSGRAAELAEVRYR
EGAAPYLSVLDAQRTLLRAQDAVAEAETASYTSLVALYKALGGGWQAPAAAGGVPTT