Protein Info for GFF5341 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 50 100 150 200 254 transmembrane" amino acids 21 to 43 (23 residues), see Phobius details amino acids 50 to 74 (25 residues), see Phobius details amino acids 86 to 106 (21 residues), see Phobius details amino acids 112 to 131 (20 residues), see Phobius details amino acids 138 to 162 (25 residues), see Phobius details amino acids 170 to 193 (24 residues), see Phobius details amino acids 225 to 246 (22 residues), see Phobius details PF01061: ABC2_membrane" amino acids 7 to 217 (211 residues), 116.8 bits, see alignment E=1e-37 PF12698: ABC2_membrane_3" amino acids 53 to 242 (190 residues), 46.4 bits, see alignment E=3.1e-16

Best Hits

Swiss-Prot: 37% identical to YADH_SHIFL: Inner membrane transport permease YadH (yadH) from Shigella flexneri

KEGG orthology group: K09686, antibiotic transport system permease protein (inferred from 95% identity to vap:Vapar_1161)

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 (254 amino acids)

>GFF5341 Efflux ABC transporter, permease protein (Variovorax sp. SCN45)
MMAVTGWRALLYKETLRFWKVGFQTVGAPVLTALLYLMVFGHVLEGRVTVYGTVGYTAFL
VPGLVMMSVLQNAFANSSSSIIQSKIMGNLVFVLLTPLSHWGWFFAYVGSSIIRGLAVGL
GVFLVTMLFAVPDFVAPLWIIVFALLGAAMLGTLGLIAGLWAEKFDQMAVFQNFLIMPMT
FLSGVFYSIGSLPPFWQKVSHLNPFFYMIDGFRYGFFGVSDASPWLSLGIVGTAWLVVSA
IAVHLLRIGYKIRG