Protein Info for GFF3608 in Variovorax sp. SCN45

Annotation: ABC transporter, permease protein 2 (cluster 4, leucine/isoleucine/valine/benzoate)

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 50 100 150 200 250 300 358 transmembrane" amino acids 21 to 39 (19 residues), see Phobius details amino acids 45 to 64 (20 residues), see Phobius details amino acids 71 to 89 (19 residues), see Phobius details amino acids 95 to 116 (22 residues), see Phobius details amino acids 123 to 142 (20 residues), see Phobius details amino acids 170 to 190 (21 residues), see Phobius details amino acids 220 to 238 (19 residues), see Phobius details amino acids 258 to 282 (25 residues), see Phobius details amino acids 303 to 325 (23 residues), see Phobius details PF02653: BPD_transp_2" amino acids 46 to 315 (270 residues), 147.6 bits, see alignment E=2e-47

Best Hits

KEGG orthology group: K01998, branched-chain amino acid transport system permease protein (inferred from 96% identity to vap:Vapar_4939)

Predicted SEED Role

"Branched-chain amino acid transport system permease protein LivM (TC 3.A.1.4.1)" in subsystem ABC transporter branched-chain amino acid (TC 3.A.1.4.1) (TC 3.A.1.4.1)

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 (358 amino acids)

>GFF3608 ABC transporter, permease protein 2 (cluster 4, leucine/isoleucine/valine/benzoate) (Variovorax sp. SCN45)
MRFIFKTSYDQDIRLARHGGHMFWYGLLVAFLLAAPWVIDEYWLAQLTFVLIYGIVGLGL
MLLAGFTGQFSIGHAAFLGAGAYTQGVLTNLGVPFPLALVAAAALSAAVGVVVALPALRV
KGIYLGIATLSFGFIVEEVFARWESVTGGNAGLHVKSPQLFGWSLGSGEGFYFLCLVVAV
LATLGILNLLRSPTGRAFVAIRDSEISAQSMGIHLARYKTMSFAISAALAGLGGALYAHK
LSFISPDQFSILQSIDLLLMVVIGGLGSVHGAFLGAIFLIAMPQLISIGKDWLPEAIGQA
PGLQGLVYGVVLIAFVLFEPLGLYGRWLKVRTWLQLFPFYRKGLFKRQKSFTKSDRLR