Protein Info for GFF6253 in Variovorax sp. SCN45

Annotation: Phosphonate ABC transporter substrate-binding protein PhnD (TC 3.A.1.9.1)

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 50 100 150 200 250 316 signal peptide" amino acids 1 to 22 (22 residues), see Phobius details TIGR03431: phosphonate ABC transporter, periplasmic phosphonate binding protein" amino acids 1 to 284 (284 residues), 345.8 bits, see alignment E=2.1e-107 TIGR01098: phosphate/phosphite/phosphonate ABC transporter, periplasmic binding protein" amino acids 5 to 247 (243 residues), 281.6 bits, see alignment E=5.7e-88 PF12974: Phosphonate-bd" amino acids 27 to 274 (248 residues), 244.3 bits, see alignment E=6.4e-77

Best Hits

Swiss-Prot: 55% identical to PHND_ECOLI: Phosphonates-binding periplasmic protein (phnD) from Escherichia coli (strain K12)

KEGG orthology group: K02044, phosphonate transport system substrate-binding protein (inferred from 92% identity to vap:Vapar_6090)

Predicted SEED Role

"Phosphonate ABC transporter phosphate-binding periplasmic component (TC 3.A.1.9.1)" in subsystem ABC transporter alkylphosphonate (TC 3.A.1.9.1) (TC 3.A.1.9.1)

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 (316 amino acids)

>GFF6253 Phosphonate ABC transporter substrate-binding protein PhnD (TC 3.A.1.9.1) (Variovorax sp. SCN45)
MIKKLLAALAIGLGMTAAAQAQDAINFGIISTEATQNLKGDWQPLIDDMSKQTGLKVTAF
FAPDYAGIIEAMRFNKVQLGWFGNKSAMEAVDRASGEVFAQMVNADGTQGYYSHLIVNRE
SPLNTLDDVLKNAKNLSFGNGDPNSTSGYLVPGFYVFAQNKVDAKTIFKITRSANHETNA
LAVANKQVDVATNNSENLEKVKERFPEKFKDIKIVWTSPLIPLDPLVMRKDLPEATKAKL
RNFFFNYAKTDAREKEIVMKISKLSGFKESSDKQLLPIRQIDLFGQRTKIEADTVLSDAD
KKAKLADIDKKLAALN