Protein Info for GFF1968 in Variovorax sp. SCN45

Annotation: Hydroxymethylpyrimidine ABC transporter, transmembrane component

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 50 100 150 200 268 transmembrane" amino acids 20 to 43 (24 residues), see Phobius details amino acids 64 to 91 (28 residues), see Phobius details amino acids 101 to 122 (22 residues), see Phobius details amino acids 128 to 150 (23 residues), see Phobius details amino acids 173 to 190 (18 residues), see Phobius details amino acids 194 to 220 (27 residues), see Phobius details amino acids 232 to 253 (22 residues), see Phobius details PF00528: BPD_transp_1" amino acids 80 to 253 (174 residues), 85.7 bits, see alignment E=1.8e-28

Best Hits

KEGG orthology group: K02050, sulfonate/nitrate/taurine transport system permease protein (inferred from 97% identity to vpe:Varpa_5417)

Predicted SEED Role

"Hydroxymethylpyrimidine ABC transporter, transmembrane component" in subsystem Thiamin biosynthesis

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 (268 amino acids)

>GFF1968 Hydroxymethylpyrimidine ABC transporter, transmembrane component (Variovorax sp. SCN45)
MKKNIPLMSQPRVQRVLYPVLIGVVLVALWQWMVVAMELPAYLVPSPYLMMQTLVTDWAP
LGNALLVTLKITVLSFLLATVAGVLISFLFVQSKRIETALFPYAVLLQVTPIVAVAPLII
IWVKNPVAAMTVCAALVALFPIISNTTLGLRSIDPDLQSYFKLNRATRWQQLVRLRIPSA
LPYFFGGLRISSGLALIGAVVAEFVAGTGGSGAGLAYQILQAGFQLNIPRMFAALLLISL
TGVALFVLMAWLTKVALGSWHASELSQD