Protein Info for GFF4300 in Sphingobium sp. HT1-2

Annotation: IncF plasmid conjugative transfer pilus assembly protein TraF

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 50 100 150 200 250 301 signal peptide" amino acids 1 to 27 (27 residues), see Phobius details TIGR02740: TraF-like protein" amino acids 63 to 294 (232 residues), 264.1 bits, see alignment E=6.9e-83 PF13728: TraF" amino acids 78 to 290 (213 residues), 236.5 bits, see alignment E=1.7e-74

Best Hits

KEGG orthology group: K12057, conjugal transfer pilus assembly protein TraF (inferred from 62% identity to swi:Swit_5381)

Predicted SEED Role

"IncF plasmid conjugative transfer pilus assembly protein TraF" in subsystem Type 4 secretion and conjugative transfer

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 (301 amino acids)

>GFF4300 IncF plasmid conjugative transfer pilus assembly protein TraF (Sphingobium sp. HT1-2)
MRNALTLALILSLATGGIAPVAGASAQELTPLLDSVSSARESEAPSSADRERDEDLGGAD
RVAAQTGDDFYCRERRLGTWFYCDKPKPKPSEQQSAQPARSSAERLAAIAKELEELKARA
ILEPTPENIAHYIAFQREQLDRASSFADMWQRTIWQNPDLDYTLQRPVNQLGKRTWLDTR
NADRERVLSQISQRYGVFYFYSSACAACETFGPIMRSISDRFGLTVMAISLDGGPTRAFP
NYTVDTGQYKAMGMRGQQVPALVLFDTVTKRPMPIGYGVMAADEVMNRIFTLTSIKPGSD
F