Protein Info for GFF3269 in Variovorax sp. SCN45

Annotation: Lipopolysaccharide export system protein LptC

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 50 100 150 220 transmembrane" amino acids 20 to 38 (19 residues), see Phobius details TIGR04409: LPS export ABC transporter periplasmic protein LptC" amino acids 20 to 204 (185 residues), 151.2 bits, see alignment E=1.1e-48 PF06835: LptC" amino acids 25 to 204 (180 residues), 94.7 bits, see alignment E=2.7e-31

Best Hits

KEGG orthology group: K11719, lipopolysaccharide export system protein LptC (inferred from 85% identity to vpe:Varpa_6013)

Predicted SEED Role

"Probable transmembrane protein"

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 (220 amino acids)

>GFF3269 Lipopolysaccharide export system protein LptC (Variovorax sp. SCN45)
MNNVKRAWGLVRNVLDRATIYLPIILTAAVALGTYWLVRNAPKLLEPTAKAAPTHEPDYF
MRDFVIKNFLPNGELRSELFGVEGRHYPDTDTIEVDKVRMRSISPEGLVTRSTANRGLSN
SDGSELQLFGNAIVIRDPSVGADGKPTPRLEFRGEFLHAFVDTERVTSNQPVTLIRDKDQ
FTGDTLDYDNLTGVANLRGRVRGVLIPSAAAAAPAPAKKR