Protein Info for PGA1_c03650 in Phaeobacter inhibens DSM 17395

Annotation: malate dehydrogenase Mdh

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 309 (307 residues), 421.6 bits, E=8.7e-131
• PF00056: Ldh_1_N
  • amino acids 5 to 143 (139 residues), 131.5 bits, E=2.4e-42
• PF02866: Ldh_1_C
  • amino acids 148 to 306 (159 residues), 115.3 bits, E=3.2e-37

Best Hits

Swiss-Prot: 93% identical to MDH_RUEPO: Malate dehydrogenase (mdh) from Ruegeria pomeroyi (strain ATCC 700808 / DSM 15171 / DSS-3)

KEGG orthology group: K00024, malate dehydrogenase [EC: 1.1.1.37] (inferred from 93% identity to sil:SPO0349)

MetaCyc: 77% 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)
• TCA cycle III (animals) (9/10 steps found)
• methylaspartate cycle (15/19 steps found)
• superpathway of glycolysis, pyruvate dehydrogenase, TCA, and glyoxylate bypass (20/26 steps found)
• superpathway of cytosolic glycolysis (plants), pyruvate dehydrogenase and TCA cycle (17/22 steps found)
• TCA cycle I (prokaryotic) (8/10 steps found)
• TCA cycle VIII (Chlamydia) (5/6 steps found)
• glyoxylate cycle (5/6 steps found)
• malate/L-aspartate shuttle pathway (2/2 steps found)
• TCA cycle II (plants and fungi) (7/9 steps found)
• TCA cycle V (2-oxoglutarate synthase) (7/9 steps found)
• gluconeogenesis III (9/12 steps found)
• superpathway of glyoxylate bypass and TCA (9/12 steps found)
• superpathway of glyoxylate cycle and fatty acid degradation (10/14 steps found)
• anaerobic energy metabolism (invertebrates, mitochondrial) (7/10 steps found)
• TCA cycle IV (2-oxoglutarate decarboxylase) (6/9 steps found)
• mixed acid fermentation (11/16 steps found)
• chitin deacetylation (2/4 steps found)
• reductive TCA cycle I (7/11 steps found)
• anaerobic energy metabolism (invertebrates, cytosol) (4/7 steps found)
• incomplete reductive TCA cycle (4/7 steps found)
• pyruvate fermentation to propanoate I (4/7 steps found)
• superpathway of anaerobic energy metabolism (invertebrates) (11/17 steps found)
• formaldehyde assimilation I (serine pathway) (8/13 steps found)
• methylgallate degradation (2/6 steps found)
• (S)-lactate fermentation to propanoate, acetate and hydrogen (7/13 steps found)
• protocatechuate degradation I (meta-cleavage pathway) (3/8 steps found)
• C4 photosynthetic carbon assimilation cycle, NAD-ME type (5/11 steps found)
• reductive TCA cycle II (5/12 steps found)
• L-glutamate degradation VIII (to propanoate) (4/11 steps found)
• superpathway of vanillin and vanillate degradation (3/10 steps found)
• syringate degradation (3/12 steps found)
• Methanobacterium thermoautotrophicum biosynthetic metabolism (21/56 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

No predicted isozymes

Use Curated BLAST to search for 1.1.1.37 or 1.1.1.38

Sequence Analysis Tools

See I7DXB6 at UniProt or InterPro

Protein Sequence (320 amino acids)

>PGA1_c03650 malate dehydrogenase Mdh (Phaeobacter inhibens DSM 17395)
MARPKIALIGAGQIGGTLAHLAALKELGDVVLFDIAEGTPEGKALDIAESGPSEGFDAKL
KGTQSYEDIAGADVCIVTAGVPRKPGMSRDDLLGINLKVMKSVGEGIRDHAPDAFVICIT
NPLDAMVWALREFSGLPHEKVCGMAGVLDSARFRHFLAEEFNVSMKDVTAFVLGGHGDTM
VPLTRYSTVAGIPLPDLVKMGWTSQEKLDAIVQRTRDGGAEIVGLLKTGSAFYAPATSAI
EMAEAYLKDQKRVLPCAAYVDGALGLKGMYVGVPTVIGAGGIERVIDIKMTSDEQTMFDN
SVNAVKGLVEACKGIDGSLA