Protein Info for GFF4411 in Xanthobacter sp. DMC5

Annotation: Malate dehydrogenase

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

• TIGR01763: malate dehydrogenase, NAD-dependent
  • amino acids 3 to 308 (306 residues), 415.1 bits, E=8.4e-129
• PF00056: Ldh_1_N
  • amino acids 5 to 143 (139 residues), 132.1 bits, E=1.6e-42
• PF02866: Ldh_1_C
  • amino acids 148 to 303 (156 residues), 122.2 bits, E=2.4e-39

Best Hits

Swiss-Prot: 93% identical to MDH_XANP2: Malate dehydrogenase (mdh) from Xanthobacter autotrophicus (strain ATCC BAA-1158 / Py2)

KEGG orthology group: K00024, malate dehydrogenase [EC: 1.1.1.37] (inferred from 93% identity to xau:Xaut_0153)

MetaCyc: 75% identical to malate dehydrogenase subunit (Methylorubrum extorquens AM1)
Malate dehydrogenase. [EC: 1.1.1.37, 1.1.1.38]

Predicted SEED Role

"Malate dehydrogenase (EC 1.1.1.37)" in subsystem Serine-glyoxylate cycle or TCA Cycle (EC 1.1.1.37)

MetaCyc Pathways

• gluconeogenesis I (12/13 steps found)
• superpathway of cytosolic glycolysis (plants), pyruvate dehydrogenase and TCA cycle (18/22 steps found)
• TCA cycle I (prokaryotic) (9/10 steps found)
• TCA cycle III (animals) (9/10 steps found)
• TCA cycle VIII (Chlamydia) (6/6 steps found)
• TCA cycle II (plants and fungi) (8/9 steps found)
• TCA cycle V (2-oxoglutarate synthase) (8/9 steps found)
• superpathway of glyoxylate bypass and TCA (10/12 steps found)
• superpathway of glycolysis, pyruvate dehydrogenase, TCA, and glyoxylate bypass (20/26 steps found)
• superpathway of glyoxylate cycle and fatty acid degradation (11/14 steps found)
• anaerobic energy metabolism (invertebrates, mitochondrial) (8/10 steps found)
• superpathway of anaerobic energy metabolism (invertebrates) (13/17 steps found)
• glyoxylate cycle (5/6 steps found)
• malate/L-aspartate shuttle pathway (2/2 steps found)
• TCA cycle IV (2-oxoglutarate decarboxylase) (7/9 steps found)
• methylaspartate cycle (14/19 steps found)
• L-malate degradation II (1/1 steps found)
• chitin deacetylation (3/4 steps found)
• C4 photosynthetic carbon assimilation cycle, NAD-ME type (8/11 steps found)
• anaerobic energy metabolism (invertebrates, cytosol) (5/7 steps found)
• mixed acid fermentation (11/16 steps found)
• gluconeogenesis III (8/12 steps found)
• pyruvate fermentation to propanoate I (4/7 steps found)
• L-carnitine degradation II (1/3 steps found)
• reductive TCA cycle I (6/11 steps found)
• incomplete reductive TCA cycle (3/7 steps found)
• methylgallate degradation (2/6 steps found)
• (S)-lactate fermentation to propanoate, acetate and hydrogen (7/13 steps found)
• formaldehyde assimilation I (serine pathway) (7/13 steps found)
• reductive TCA cycle II (6/12 steps found)
• protocatechuate degradation I (meta-cleavage pathway) (3/8 steps found)
• superpathway of vanillin and vanillate degradation (4/10 steps found)
• L-glutamate degradation VIII (to propanoate) (4/11 steps found)
• syringate degradation (3/12 steps found)
• Methanobacterium thermoautotrophicum biosynthetic metabolism (25/56 steps found)

KEGG Metabolic Maps

• Biosynthesis of alkaloids derived from histidine and purine
• Biosynthesis of alkaloids derived from ornithine, lysine and nicotinic acid
• Biosynthesis of alkaloids derived from shikimate pathway
• Biosynthesis of alkaloids derived from terpenoid and polyketide
• Biosynthesis of phenylpropanoids
• Biosynthesis of plant hormones
• Biosynthesis of terpenoids and steroids
• Carbon fixation in photosynthetic organisms
• Citrate cycle (TCA cycle)
• Glyoxylate and dicarboxylate metabolism
• Pyruvate metabolism
• Reductive carboxylate cycle (CO2 fixation)

Isozymes

Compare fitness of predicted isozymes for: 1.1.1.37, 1.1.1.38

Use Curated BLAST to search for 1.1.1.37 or 1.1.1.38

Protein Sequence (321 amino acids)

>GFF4411 Malate dehydrogenase (Xanthobacter sp. DMC5)
MARNKIALIGAGQIGGTLALLAGLKELGDIVLFDVADGVPDGKALDLAQLTPVEGFDAGI
WGASSYDAIAGADVVIVTAGVPRKPGMSRDDLLAINLKVMEQVGAGLRKYAPDAFVICIT
NPLDAMVWALQRTSGLPPEKVVGMAGVLDSARFRFFLSEEFGVSVEDVTAFVMGGHGDTM
VPLVRYSAVGGIPVPDLIRMGWTSEERIAAIVQRVRDGGAEIVNLLKTGSAFYAPAAAAI
AMAESYLKDKKRVLPVAARLDGEYGLRDIYLGVPAVIGARGVERIVEVELDRSERAMFER
SVAAVEGLVEACLKIAPGLGK