Protein Info for GFF3572 in Variovorax sp. SCN45

Annotation: Efflux ABC transporter, permease protein

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 50 100 150 200 250 275 transmembrane" amino acids 44 to 67 (24 residues), see Phobius details amino acids 78 to 101 (24 residues), see Phobius details amino acids 131 to 154 (24 residues), see Phobius details amino acids 161 to 185 (25 residues), see Phobius details amino acids 191 to 210 (20 residues), see Phobius details amino acids 217 to 239 (23 residues), see Phobius details amino acids 247 to 268 (22 residues), see Phobius details TIGR01291: ABC-2 type transporter, NodJ family" amino acids 22 to 273 (252 residues), 207 bits, see alignment E=1.8e-65 PF01061: ABC2_membrane" amino acids 42 to 237 (196 residues), 54.8 bits, see alignment E=9.8e-19 PF12698: ABC2_membrane_3" amino acids 78 to 266 (189 residues), 31.9 bits, see alignment E=7.8e-12

Best Hits

Swiss-Prot: 42% identical to NODJ_RHILV: Nodulation protein J (nodJ) from Rhizobium leguminosarum bv. viciae

KEGG orthology group: K09694, lipooligosaccharide transport system permease protein (inferred from 93% identity to vpe:Varpa_5648)

Predicted SEED Role

"ABC-type multidrug transport system, permease component"

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 (275 amino acids)

>GFF3572 Efflux ABC transporter, permease protein (Variovorax sp. SCN45)
MNTTTTTNAPASPSVWRAPEISLRWWPVFLRNLLVWRKLAIPSLIGNIAEPLIWLVAFGY
GMGALVGQVSVDDVKVPYILFLASGSICMSAMNAASFEALYSAFSRMHVQKTWDGIMNAP
VGLDDIVLAEMLWAAFKSIFTVTAILFVMLGLGISHSPKLVVAWMVLVGAGITFSSVALI
FNALAKGYDFFTYYFTLFMTPMMFLSGVFFPLEQLPAAVRAVAAWLPLTNAVALVRPLFM
DQWPTGWWVHAAVLAVYAVVAFWIALALTRKRFKG