Protein Info for GFF38 in Xanthobacter sp. DMC5

Annotation: Inner membrane ABC transporter permease protein YdcV

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 50 100 150 200 264 transmembrane" amino acids 12 to 33 (22 residues), see Phobius details amino acids 64 to 90 (27 residues), see Phobius details amino acids 102 to 124 (23 residues), see Phobius details amino acids 129 to 151 (23 residues), see Phobius details amino acids 189 to 211 (23 residues), see Phobius details amino acids 232 to 252 (21 residues), see Phobius details PF00528: BPD_transp_1" amino acids 79 to 252 (174 residues), 52.9 bits, see alignment E=1.9e-18

Best Hits

Swiss-Prot: 34% identical to MODB_MYCBO: Molybdenum transport system permease protein ModB (modB) from Mycobacterium bovis (strain ATCC BAA-935 / AF2122/97)

KEGG orthology group: K02053, putative spermidine/putrescine transport system permease protein (inferred from 81% identity to azc:AZC_1799)

Predicted SEED Role

"ABC opine/polyamine transporter, inner membrane subunit"

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 (264 amino acids)

>GFF38 Inner membrane ABC transporter permease protein YdcV (Xanthobacter sp. DMC5)
MDERPVSPALKIAAGLMFLFLLAPLLVVLPISFSGDDFMAFPPSSWSVKWYGAIFANSVM
MNAFWISLALAFVVTALSLGIGLPAAYALVRLKPPGAEALSNLFSAPLLLPTIVLGLALL
LVFAPMGLIGSFQGLVAAHLIVTLPYAVRVLSTALANLPLTVEEAAGMLGARPLTVFFRV
TLPMMRSGLVSTTALCFLVSFDEVVLSLFMTGPRLQTLPVAMYNHVDQQADPMAAAISVL
LVVLTLAVVLVVDRTAGLTRTFVK