Protein Info for Shew_1163 in Shewanella loihica PV-4

Annotation: RND family efflux transporter MFP subunit (RefSeq)

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 50 100 150 200 250 300 350 385 signal peptide" amino acids 1 to 34 (34 residues), see Phobius details TIGR01730: efflux transporter, RND family, MFP subunit" amino acids 40 to 371 (332 residues), 243.6 bits, see alignment E=1.3e-76 PF25917: BSH_RND" amino acids 63 to 199 (137 residues), 64.5 bits, see alignment E=1.3e-21 PF25876: HH_MFP_RND" amino acids 102 to 172 (71 residues), 38.2 bits, see alignment E=2.8e-13 PF25944: Beta-barrel_RND" amino acids 207 to 295 (89 residues), 51.7 bits, see alignment E=2e-17 PF25967: RND-MFP_C" amino acids 301 to 362 (62 residues), 70.4 bits, see alignment E=2e-23

Best Hits

Swiss-Prot: 32% identical to MDTE_ECOLI: Multidrug resistance protein MdtE (mdtE) from Escherichia coli (strain K12)

KEGG orthology group: K03585, membrane fusion protein (inferred from 100% identity to slo:Shew_1163)

MetaCyc: 32% identical to multidrug efflux pump membrane fusion protein MdtE (Escherichia coli K-12 substr. MG1655)
TRANS-RXN-352; TRANS-RXN-359; TRANS-RXN-367

Predicted SEED Role

"Membrane fusion protein of RND family multidrug efflux pump" in subsystem Multidrug Resistance Efflux Pumps

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

See A3QC35 at UniProt or InterPro

Protein Sequence (385 amino acids)

>Shew_1163 RND family efflux transporter MFP subunit (RefSeq) (Shewanella loihica PV-4)
MLGRNASPLARLTLFSAALLLAACGKAPAPGPAVMPSVIVNTAQVKEIRAKTEIVGRTRA
SEDVVIKSQIQGQLLKRTFVEGDDIDAGELLFEIDPSTFEAELAQQQAVLKQAIASRDVA
VMNWERGRRLLPDGMISAQDMDELTSRKLTTAAGVVQAEAAVKAAELQLSYTKVYAPISG
RISGAKVSQGDIITPQSELASLVQLQPMWVNFQVAEKTIISAKQNFSKAAKHEVKISDIV
IRLRLPNGTMFDETGYIDFISNRVDAATGTLELRATFNNESKLMLPGLFVTLVIESPISE
QAILIPQAAVQEDQQGRFVMVLDGDNKVQKRVVELGDRFGVDWRVLSGLNEGERIVVDGL
QKIRPGIEVKAVEQQAVPFQEANDA