Protein Info for GFF228 in Variovorax sp. SCN45

Annotation: ABC transporter, permease protein 1 (cluster 5, nickel/peptides/opines)

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 50 100 150 200 250 300 346 transmembrane" amino acids 9 to 30 (22 residues), see Phobius details amino acids 122 to 143 (22 residues), see Phobius details amino acids 155 to 180 (26 residues), see Phobius details amino acids 208 to 231 (24 residues), see Phobius details amino acids 266 to 289 (24 residues), see Phobius details amino acids 315 to 339 (25 residues), see Phobius details PF00528: BPD_transp_1" amino acids 137 to 344 (208 residues), 122.7 bits, see alignment E=7.6e-40

Best Hits

Swiss-Prot: 54% identical to YEJB_ECOLI: Inner membrane ABC transporter permease protein YejB (yejB) from Escherichia coli (strain K12)

KEGG orthology group: K13894, microcin C transport system permease protein (inferred from 96% identity to vpe:Varpa_2843)

MetaCyc: 54% identical to putative oligopeptide ABC transporter membrane subunit YejB (Escherichia coli K-12 substr. MG1655)
3.6.3.23-RXN [EC: 7.4.2.6]

Predicted SEED Role

"Oligopeptide transport system permease protein OppB (TC 3.A.1.5.1)" in subsystem ABC transporter oligopeptide (TC 3.A.1.5.1) (TC 3.A.1.5.1)

Isozymes

No predicted isozymes

Use Curated BLAST to search for 7.4.2.6

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 (346 amino acids)

>GFF228 ABC transporter, permease protein 1 (cluster 5, nickel/peptides/opines) (Variovorax sp. SCN45)
VLSYVLKRLLLFIPTLLGVLLVTFLVIQFVPGGPVEQYLAEAKTAGRGGGGGGFESGGGS
YRGNQGVDPKRLEQIKALYGFDKPPHERLWQMLGQFARFDLGKSFFQNKDVWTLILEKLP
VSISLGLWTFFISYGVAVPLGVAKAVRAGTRFDLISTLIVLIGYAIPGFVLGVALLVVFG
GQLQWFPLRGLTSANWDDLSWGARIVDYLWHITLPVTAMVLGSFAVTAMLTKNAFLEEIR
KQYVLTARAKGLGERQVLWKHVFRNALIPIITGLPSAFIGAFFAGSLLIETLFSLDGLGL
LGYESVIRRDYPVVLGTLYLFTLIGLVTKLISDLCYVWVDPRVKFE