Protein Info for GFF5989 in Variovorax sp. SCN45

Annotation: RND efflux system, membrane fusion protein

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 50 100 150 200 250 300 350 414 signal peptide" amino acids 1 to 45 (45 residues), see Phobius details PF00529: CusB_dom_1" amino acids 55 to 381 (327 residues), 27.3 bits, see alignment E=5.5e-10 TIGR01730: efflux transporter, RND family, MFP subunit" amino acids 57 to 395 (339 residues), 271.1 bits, see alignment E=5.5e-85 PF16576: HlyD_D23" amino acids 81 to 312 (232 residues), 37 bits, see alignment E=4.6e-13 PF13533: Biotin_lipoyl_2" amino acids 83 to 129 (47 residues), 32.2 bits, see alignment 1.5e-11 PF13437: HlyD_3" amino acids 193 to 310 (118 residues), 26.4 bits, see alignment E=1.9e-09

Best Hits

Swiss-Prot: 49% identical to ACRA_ECO57: Multidrug efflux pump subunit AcrA (acrA) from Escherichia coli O157:H7

KEGG orthology group: K03585, membrane fusion protein (inferred from 62% identity to vpe:Varpa_1499)

MetaCyc: 49% identical to multidrug efflux pump membrane fusion lipoprotein AcrA (Escherichia coli K-12 substr. MG1655)
TRANS-RXN-1551; TRANS-RXN-1552; TRANS-RXN-354; TRANS-RXN-355; TRANS-RXN-356; TRANS-RXN-357; TRANS-RXN-359; TRANS-RXN-360; TRANS-RXN0-592

Predicted SEED Role

"RND efflux system, membrane fusion protein CmeA" 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)

Compare to protein 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 (414 amino acids)

>GFF5989 RND efflux system, membrane fusion protein (Variovorax sp. SCN45)
MDSNLIGILNMSSRFIRTGLACALAIGLLGAIAGCSGSSSSSSALPGAPQGLAAAQVGVV
TVQPENQPVTTELSGRTRSRLSAEIRPQVGGIVQQRLFEEGALVKAGQVLYQLDPASYKA
AYASAQASVAKSEATVNAAKVTARRNAELAKIEAVSKQTSEDSQATLQQAEADLGVARAA
LETARINLGFTRITAPIAGRIEASTVTPGALVTASQTTALTTVQQLDPVYVDVTQSTTEL
LQLQRELAAGTLKNGSADKAEASVKLLLEDGTTYAHAGRLQFSSVTVNEGTGAVTLRILV
PNPERTLLPGMYMRAVLEQGVAEGALLVPQQGVTRTANGDASALVVTSENKVEKRALKVS
RAVGNRWQVIEGLKAGERVIVEGSLKVKAGDTVKAVDAAGATTVAGAQASTTAR