Protein Info for GFF2424 in Variovorax sp. SCN45

Annotation: ABC transporter, permease protein 1 (cluster 1, maltose/g3p/polyamine/iron)

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 50 100 150 200 250 283 signal peptide" amino acids 1 to 30 (30 residues), see Phobius details transmembrane" amino acids 69 to 91 (23 residues), see Phobius details amino acids 101 to 125 (25 residues), see Phobius details amino acids 149 to 174 (26 residues), see Phobius details amino acids 195 to 224 (30 residues), see Phobius details amino acids 252 to 272 (21 residues), see Phobius details PF00528: BPD_transp_1" amino acids 84 to 277 (194 residues), 42.6 bits, see alignment E=2.9e-15

Best Hits

Swiss-Prot: 35% identical to POTB_SHIFL: Spermidine/putrescine transport system permease protein PotB (potB) from Shigella flexneri

KEGG orthology group: K02054, putative spermidine/putrescine transport system permease protein (inferred from 66% identity to pde:Pden_5049)

MetaCyc: 35% identical to spermidine preferential ABC transporter membrane subunit PotB (Escherichia coli K-12 substr. MG1655)
ABC-25-RXN [EC: 7.6.2.11, 7.6.2.16]; 7.6.2.11 [EC: 7.6.2.11, 7.6.2.16]

Predicted SEED Role

"Spermidine Putrescine ABC transporter permease component PotB (TC 3.A.1.11.1)" in subsystem Polyamine Metabolism (TC 3.A.1.11.1)

Isozymes

No predicted isozymes

Use Curated BLAST to search for 7.6.2.11 or 7.6.2.16

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 (283 amino acids)

>GFF2424 ABC transporter, permease protein 1 (cluster 1, maltose/g3p/polyamine/iron) (Variovorax sp. SCN45)
MNPRKLTGALLASPLLLLLLLAFVAPVLLMVPLSLHPYEPGTGISAGWTLANYTSIVTDE
YYREVVVRTLVLGFGVTAICLLLGYPLAYYIANAGPRMRLALTMLVIFPMLLNLVVRSFG
WIALLANRGLVNNLLIDIGLIERPIKMMFNLFGLLVGMSHIFLPFMVLMLVPAIQAISKD
VQAAAYTLAASRLRVFWSITLPMSAPGILSGSILVFVLTISALVTPRMLGGPTYKVMATL
IYDDFLQTLDWPAGAAMSFALTALTLAVIGLSSRVLKRWGGNA