Protein Info for HMPREF1078_RS13680 in Parabacteroides merdae CL09T00C40

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 2 to 305 (304 residues), 370.3 bits, E=3.5e-115
• PF00056: Ldh_1_N
  • amino acids 3 to 143 (141 residues), 144.7 bits, E=2e-46
• PF02866: Ldh_1_C
  • amino acids 148 to 305 (158 residues), 95.5 bits, E=3.9e-31

Best Hits

Swiss-Prot: 99% identical to MDH_PARD8: Malate dehydrogenase (mdh) from Parabacteroides distasonis (strain ATCC 8503 / DSM 20701 / CIP 104284 / JCM 5825 / NCTC 11152)

KEGG orthology group: K00024, malate dehydrogenase [EC: 1.1.1.37] (inferred from 99% identity to pdi:BDI_0389)

MetaCyc: 41% 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 (11/13 steps found)
• gluconeogenesis III (10/12 steps found)
• malate/L-aspartate shuttle pathway (2/2 steps found)
• TCA cycle V (2-oxoglutarate synthase) (7/9 steps found)
• superpathway of cytosolic glycolysis (plants), pyruvate dehydrogenase and TCA cycle (16/22 steps found)
• reductive TCA cycle I (8/11 steps found)
• incomplete reductive TCA cycle (5/7 steps found)
• pyruvate fermentation to propanoate I (5/7 steps found)
• glyoxylate cycle (4/6 steps found)
• (S)-lactate fermentation to propanoate, acetate and hydrogen (9/13 steps found)
• TCA cycle IV (2-oxoglutarate decarboxylase) (6/9 steps found)
• mixed acid fermentation (11/16 steps found)
• anaerobic energy metabolism (invertebrates, cytosol) (4/7 steps found)
• TCA cycle I (prokaryotic) (6/10 steps found)
• TCA cycle III (animals) (6/10 steps found)
• TCA cycle VIII (Chlamydia) (3/6 steps found)
• TCA cycle II (plants and fungi) (5/9 steps found)
• superpathway of glycolysis, pyruvate dehydrogenase, TCA, and glyoxylate bypass (17/26 steps found)
• chitin deacetylation (1/4 steps found)
• anaerobic energy metabolism (invertebrates, mitochondrial) (5/10 steps found)
• methylgallate degradation (2/6 steps found)
• formaldehyde assimilation I (serine pathway) (7/13 steps found)
• reductive TCA cycle II (6/12 steps found)
• superpathway of glyoxylate bypass and TCA (6/12 steps found)
• protocatechuate degradation I (meta-cleavage pathway) (3/8 steps found)
• C4 photosynthetic carbon assimilation cycle, NAD-ME type (5/11 steps found)
• L-glutamate degradation VIII (to propanoate) (5/11 steps found)
• superpathway of anaerobic energy metabolism (invertebrates) (9/17 steps found)
• methylaspartate cycle (10/19 steps found)
• superpathway of glyoxylate cycle and fatty acid degradation (6/14 steps found)
• superpathway of vanillin and vanillate degradation (3/10 steps found)
• syringate degradation (3/12 steps found)
• Methanobacterium thermoautotrophicum biosynthetic metabolism (19/56 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

Use Curated BLAST to search for 1.1.1.37 or 1.1.1.38

Protein Sequence (313 amino acids)

>HMPREF1078_RS13680 malate dehydrogenase (Parabacteroides merdae CL09T00C40)
MSKVTVVGAGNVGATCANVLAFNEVADEVVMLDVKEGVSEGKAMDMMQTAQLLGFDTTVT
GCTNDYEKTANSDVVVITSGIPRKPGMTREELIGVNAGIVKSVAQNILKYSPNAILVVIS
NPMDTMTYLSLKSLGLPKNRIIGMGGALDSSRFKYFLSQALGCNANEVEGMVIGGHGDTT
MIPLARLATYKGIPVSKLLSAEKLQEVVASTMVGGATLTKLLGTSAWYAPGAAGAYVVES
IIHNQKKMVPCSVYLEGEYGESDLCIGVPVILGKNGIEKIVELELTAEEKELFAKSAAAV
HKTNEALKEVGAL