Protein Info for GFF4236 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 50 100 150 200 250 300 transmembrane" amino acids 42 to 62 (21 residues), see Phobius details amino acids 104 to 124 (21 residues), see Phobius details amino acids 136 to 158 (23 residues), see Phobius details amino acids 164 to 186 (23 residues), see Phobius details amino acids 214 to 238 (25 residues), see Phobius details amino acids 258 to 278 (21 residues), see Phobius details PF00528: BPD_transp_1" amino acids 116 to 285 (170 residues), 100.1 bits, see alignment E=6.8e-33

Best Hits

KEGG orthology group: K02050, sulfonate/nitrate/taurine transport system permease protein (inferred from 47% identity to bbt:BBta_1169)

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 (300 amino acids)

>GFF4236 Hydroxymethylpyrimidine ABC transporter, transmembrane component (Variovorax sp. SCN45)
MTTAMLAKTDSVASSDDRASPPAAAAIQAKPKRRANPLASTRVQSILLLAALLGAWEAAV
RLFKVPQHLVPPVSDIVVALWRGLATGPLAKDGFWYHGGVTVTEILLGFLIGSGVGLAIG
IVVSQMPKVEALLEPYVAALQSVPKVAVAPIIVVWLGFGIGSKVMIICLLTFFPVLVTSI
AGFKAVDPDRIDLLRSLSATPWQIFRKAKFPSALPYIFAGLNMAAAFSVVGAVVGEFVGA
QAGLGVLILQMEAQADTGGSFAVCVVLSVIGIVLSSLLRRIQRRVLHWMPADASQRTVNA