Protein Info for GFF4950 in Variovorax sp. SCN45

Annotation: ABC transporter, permease protein (cluster 2, ribose/xylose/arabinose/galactose)

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 50 100 150 200 250 300 342 transmembrane" amino acids 38 to 58 (21 residues), see Phobius details amino acids 65 to 86 (22 residues), see Phobius details amino acids 92 to 109 (18 residues), see Phobius details amino acids 115 to 136 (22 residues), see Phobius details amino acids 144 to 163 (20 residues), see Phobius details amino acids 183 to 205 (23 residues), see Phobius details amino acids 236 to 255 (20 residues), see Phobius details amino acids 262 to 283 (22 residues), see Phobius details amino acids 290 to 309 (20 residues), see Phobius details amino acids 315 to 335 (21 residues), see Phobius details PF02653: BPD_transp_2" amino acids 65 to 329 (265 residues), 124 bits, see alignment E=3.1e-40

Best Hits

Swiss-Prot: 34% identical to ALSC_ECOLI: D-allose transport system permease protein AlsC (alsC) from Escherichia coli (strain K12)

KEGG orthology group: K10440, ribose transport system permease protein (inferred from 93% identity to vap:Vapar_0371)

MetaCyc: 34% identical to D-allose ABC transporter membrane subunit (Escherichia coli K-12 substr. MG1655)
ABC-42-RXN [EC: 7.5.2.8]

Predicted SEED Role

"Ribose ABC transport system, permease protein RbsC (TC 3.A.1.2.1)" in subsystem D-ribose utilization (TC 3.A.1.2.1)

Isozymes

No predicted isozymes

Use Curated BLAST to search for 7.5.2.8

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 (342 amino acids)

>GFF4950 ABC transporter, permease protein (cluster 2, ribose/xylose/arabinose/galactose) (Variovorax sp. SCN45)
MNYPAQLDAGAAPGLQPHQSGGGPVKPASKLGSMREMGLLLIIAALCVGMSFASPYFLTW
DNVRAMLLSFSIEGIVVVGMTILLIVGGIDLSVGSVVCFAMVVTGKLFLMGFDPWTAGLV
AIGASALIGAMIGGCVTRIGLNHFIASLAFMVIVRGLCLALTQGTPQSLFSLPAEFKFIG
QGTLFGIPAVILIFLLIVVVSDFVLRRSTLLRRVFYTGSNEKAALYSGIRVGHVKFWVTV
LCSASAGLAGVIYTARFGAATPTFGMGMELNVIAAAVIGGASLKGGSGTVLGAVLGLALL
SVVTSSLILLDVSPYWQDVIKGLILLAAVTIDHIMNTRKTKR