Protein Info for GFF2139 in Xanthobacter sp. DMC5

Annotation: L-rhamnonate dehydratase

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

Best Hits

Swiss-Prot: 81% identical to RHMD_PARPJ: L-rhamnonate dehydratase (rhmD) from Paraburkholderia phytofirmans (strain DSM 17436 / LMG 22146 / PsJN)

KEGG orthology group: K12661, L-rhamnonate dehydratase [EC: 4.2.1.90] (inferred from 82% identity to mno:Mnod_6625)

MetaCyc: 78% identical to L-rhamnonate dehydratase (Sphingomonas sp. SKA58)
L-rhamnonate dehydratase. [EC: 4.2.1.90]

Predicted SEED Role

"Gluconate dehydratase (EC 4.2.1.39)" in subsystem Entner-Doudoroff Pathway (EC 4.2.1.39)

MetaCyc Pathways

Entner-Doudoroff pathway III (semi-phosphorylative) (7/9 steps found)
L-rhamnose degradation III (4/7 steps found)
Entner-Doudoroff pathway II (non-phosphorylative) (5/9 steps found)
L-rhamnose degradation II (3/8 steps found)

KEGG Metabolic Maps

Isozymes

No predicted isozymes

Use Curated BLAST to search for 4.2.1.39 or 4.2.1.90

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 (394 amino acids)

>GFF2139 L-rhamnonate dehydratase (Xanthobacter sp. DMC5)
MAMPTIKAVRAYTVRGGGADYHDTQGYHWIDDHIATPMARYEEYRQSRRSFGINVLGTLV
VEVEASDGTIGLGVTTAGEIGAFIVEKHLSRFLIGRQVTEIEKIWDQMYFSTQFYGRKGV
VVNTISGVDIALWDLLGKLRGEPVHALLGGPVRDELQFYATGARPDLAKEMGFIGGKLPL
LHGPAEGDEGLKKNIEKLADMRSKVGDDFWLMYDCWMSLDLNYSIRLAQKAQEFGLKWIE
ECLSPDDYWGYADLKRNVPKGMLVTTGEHEATRWGFRMLLEMDCCDIIQPDVNWCGGITE
LIKISALADAHGKLMVPHGSGVYSYHFVITRHNSPFTEIIMSAPNADEVRPAFSPLLLDE
PVPVNGRMKASALDKPGFGVRLNPEVQLHRPYAP