Protein Info for GFF5648 in Variovorax sp. SCN45

Annotation: ABC transporter, substrate-binding protein (cluster 12, methionine/phosphonates)

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 50 100 150 200 250 286 signal peptide" amino acids 1 to 25 (25 residues), see Phobius details TIGR01098: phosphate/phosphite/phosphonate ABC transporter, periplasmic binding protein" amino acids 2 to 245 (244 residues), 239.1 bits, see alignment E=5.5e-75 TIGR04553: putative selenate ABC transporter periplasmic binding protein" amino acids 27 to 286 (260 residues), 366.3 bits, see alignment E=8.8e-114 PF12974: Phosphonate-bd" amino acids 31 to 272 (242 residues), 242.9 bits, see alignment E=3.2e-76 PF09084: NMT1" amino acids 54 to 199 (146 residues), 27.1 bits, see alignment E=3.9e-10

Best Hits

Swiss-Prot: 37% identical to PHND1_PROM0: Probable ABC transporter phosphite binding protein PhnD1 (phnD1) from Prochlorococcus marinus (strain MIT 9301)

KEGG orthology group: K02044, phosphonate transport system substrate-binding protein (inferred from 95% identity to vpe:Varpa_4727)

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 (286 amino acids)

>GFF5648 ABC transporter, substrate-binding protein (cluster 12, methionine/phosphonates) (Variovorax sp. SCN45)
MMKKTFTRLALALSLSAASLGAFAQGVLRVSAIPDEAPTELQRKFTPLGDYLKKETGMDV
QFTPVTDYAAVVEGLATNKIDLAWLGGFTFVQARIRTNGGAVPIVQRAEDEVFTSKFIVP
VDSTAKTLADLKGKTFAFGAPSSTSGSLMPRYFLLQAGINPEKDFKTVAFSGAHDATVAF
VAASRAEAGVLNASVWDKLVEAKNPNAAKVRVLATTPTYYDYNWTVRPGLDPALTRKLAD
AFLKLDPANPAHKEIMALQRASKFIPTKSSNYDGIETAGKSAGLIK