Protein Info for GFF987 in Variovorax sp. SCN45

Annotation: Outer membrane beta-barrel assembly protein BamD

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 50 100 150 200 268 signal peptide" amino acids 1 to 27 (27 residues), see Phobius details TIGR03302: outer membrane assembly lipoprotein YfiO" amino acids 11 to 252 (242 residues), 276.5 bits, see alignment E=8.8e-87 PF13512: TPR_18" amino acids 30 to 172 (143 residues), 123.8 bits, see alignment E=9.8e-40 PF13525: YfiO" amino acids 36 to 241 (206 residues), 188.4 bits, see alignment E=2e-59 PF13432: TPR_16" amino acids 41 to 108 (68 residues), 28.7 bits, see alignment E=2.4e-10 amino acids 78 to 122 (45 residues), 15.9 bits, see alignment 2.4e-06

Best Hits

Swiss-Prot: 45% identical to BAMD_NEIMA: Outer membrane protein assembly factor BamD (bamD) from Neisseria meningitidis serogroup A / serotype 4A (strain Z2491)

KEGG orthology group: K05807, putative lipoprotein (inferred from 94% identity to vap:Vapar_2179)

Predicted SEED Role

"Probable component of the lipoprotein assembly complex (forms a complex with YaeT, YfgL, and NlpB)"

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 (268 amino acids)

>GFF987 Outer membrane beta-barrel assembly protein BamD (Variovorax sp. SCN45)
MFRAKLSVPTWIALSAVALLAAGCSSTSVDKTANWSPNKIYAEAKDEAGSGAYDKAVPLY
EKLEGRAAGTPLAQQAQLEKAYAQYKSGEKASAIATIDRFMKLHPASPALDYALYLKGVI
NFNDDLGMFAFLTRQDLSERDQKAAKESFESFKDLVTRFPESRYAPDSRQRMNYIVNSLA
QYEVHVARYYYSRGAYLAAINRAQIALSDYREVPALEEALYIMVKSYDALGMKDLRDDAQ
RVLTTNYPQSTYLANGFKGKDDPWWKVW