Protein Info for GFF6468 in Variovorax sp. SCN45

Annotation: TRAP-type transport system, periplasmic component, predicted N-acetylneuraminate-binding 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 50 100 150 200 250 322 signal peptide" amino acids 1 to 22 (22 residues), see Phobius details PF03480: DctP" amino acids 29 to 308 (280 residues), 309.7 bits, see alignment E=9.9e-97 TIGR00787: TRAP transporter solute receptor, DctP family" amino acids 30 to 281 (252 residues), 263.6 bits, see alignment E=9.1e-83

Best Hits

Swiss-Prot: 85% identical to DCTP_VEREI: Solute-binding protein Veis_3954 (Veis_3954) from Verminephrobacter eiseniae (strain EF01-2)

KEGG orthology group: None (inferred from 95% identity to vap:Vapar_3295)

MetaCyc: 41% identical to 2,3-diketo-L-gulonate:Na+ symporter - periplasmic binding protein (Escherichia coli K-12 substr. MG1655)
TRANS-RXN0-235

Predicted SEED Role

"TRAP-type transport system, periplasmic component, predicted N-acetylneuraminate-binding protein" in subsystem Sialic Acid Metabolism

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 (322 amino acids)

>GFF6468 TRAP-type transport system, periplasmic component, predicted N-acetylneuraminate-binding protein (Variovorax sp. SCN45)
MKFGPIAAACLSLALSSVAFAQTTMKISISTAQNSHQGVAIDTFAKEVEKRTGGRYKVQT
FYNGSLGGERESIEAVQLGTQELAFSSTGPVPNFVPETKILDVPFLFRDKAHARAVLDGP
IGQDMLTKFDAKGFKALAWAENGFRHMTNSKRDVKAPEDLKGLKMRTMENPVHIAAYKGF
GIITTPMAFPEVFTALQQGTVDGQENPLPVIISAKFDQVQKHLSLTGHVYSPCIFVMNKA
TFDKLSAADKQAFLDAAKEGTKANRARVDEDDAKGVADLRAKGMTVVDNVDKARFVAALA
PVNAQFEKDFGKANLDKIRDYK