Protein Info for GFF2028 in Xanthobacter sp. DMC5

Annotation: D-malate dehydrogenase [decarboxylating]

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: 68% identical to DMLA_ECOLI: D-malate dehydrogenase [decarboxylating] (dmlA) from Escherichia coli (strain K12)

KEGG orthology group: K07246, tartrate dehydrogenase/decarboxylase / D-malate dehydrogenase [EC: 1.1.1.83 1.1.1.93 4.1.1.73] (inferred from 79% identity to npp:PP1Y_Mpl4131)

MetaCyc: 77% identical to L-tartrate dehydrogenase/D-malate dehydrogenase (decarboxylating)/meso-tartrate decarboxylase monomer (Cereibacter sphaeroides)
4.1.1.M27 [EC: 4.1.1.M27]; Tartrate dehydrogenase. [EC: 4.1.1.M27, 1.1.1.93, 4.1.1.73]; D-malate dehydrogenase (decarboxylating). [EC: 4.1.1.M27, 1.1.1.93, 4.1.1.73, 1.1.1.83]

Predicted SEED Role

"Tartrate dehydrogenase (EC 1.1.1.93) @ Tartrate decarboxylase (EC 4.1.1.73) @ D-malic enzyme (EC 1.1.1.83)" (EC 1.1.1.83, EC 1.1.1.93, EC 4.1.1.73)

MetaCyc Pathways

D-malate degradation (1/1 steps found)
gentisate degradation II (1/4 steps found)
methylgallate degradation (2/6 steps found)
protocatechuate degradation I (meta-cleavage pathway) (3/8 steps found)
superpathway of vanillin and vanillate degradation (4/10 steps found)
syringate degradation (3/12 steps found)

KEGG Metabolic Maps

Isozymes

No predicted isozymes

Use Curated BLAST to search for 1.1.1.83 or 1.1.1.93 or 4.1.1.73 or 4.1.1.M27

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 (357 amino acids)

>GFF2028 D-malate dehydrogenase [decarboxylating] (Xanthobacter sp. DMC5)
MAGRHYRIAVIPGDGIGKEVMPEGVRVLEKAAALYGFSLDLNWHDFACCDYYARHGEMMP
ADWKERVGTSDAILFGAVGWPDTVPDHVSLWGSLLQFRREFDQYVNLRPVRLMPGVPSPL
VGRKPGDIDFWVVRENTEGEYTSIGGRMYPGTSRELVIQETVMSRHGVDRVLKFAFELAM
RRPNRHLTSATKSNGIAITMPYWDERVEAMAASYPEVRTDKYHIDILTAQFVLHPDRFDV
VVASNLFGDILSDLGPACTGTIGIAPSGNINPDRTFPSLFEPVHGSAPDIAGKGVANPVG
QIWSAAMMLEHLGEMDAAAAIERAIERVLAEPAGRTADIGGTANTLSCGKAIADALD