Protein Info for DZA65_RS03130 in Dickeya dianthicola ME23
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
Best Hits
Swiss-Prot: 90% identical to MDH_ECOL6: Malate dehydrogenase (mdh) from Escherichia coli O6:H1 (strain CFT073 / ATCC 700928 / UPEC)
KEGG orthology group: K00024, malate dehydrogenase [EC: 1.1.1.37] (inferred from 99% identity to ddd:Dda3937_03529)MetaCyc: 90% identical to malate dehydrogenase (Escherichia coli K-12 substr. MG1655)
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
- superpathway of glycolysis, pyruvate dehydrogenase, TCA, and glyoxylate bypass (25/26 steps found)
- gluconeogenesis I (13/13 steps found)
- mixed acid fermentation (15/16 steps found)
- superpathway of glyoxylate bypass and TCA (11/12 steps found)
- superpathway of cytosolic glycolysis (plants), pyruvate dehydrogenase and TCA cycle (18/22 steps found)
- TCA cycle I (prokaryotic) (9/10 steps found)
- glyoxylate cycle (6/6 steps found)
- superpathway of glyoxylate cycle and fatty acid degradation (11/14 steps found)
- TCA cycle III (animals) (8/10 steps found)
- TCA cycle VIII (Chlamydia) (5/6 steps found)
- formaldehyde assimilation I (serine pathway) (10/13 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)
- 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)
- reductive TCA cycle I (8/11 steps found)
- anaerobic energy metabolism (invertebrates, cytosol) (5/7 steps found)
- incomplete reductive TCA cycle (5/7 steps found)
- TCA cycle IV (2-oxoglutarate decarboxylase) (6/9 steps found)
- reductive TCA cycle II (8/12 steps found)
- L-carnitine degradation II (1/3 steps found)
- (S)-lactate fermentation to propanoate, acetate and hydrogen (8/13 steps found)
- pyruvate fermentation to propanoate I (3/7 steps found)
- anaerobic energy metabolism (invertebrates, mitochondrial) (5/10 steps found)
- superpathway of anaerobic energy metabolism (invertebrates) (10/17 steps found)
- methylgallate degradation (2/6 steps found)
- protocatechuate degradation I (meta-cleavage pathway) (3/8 steps found)
- superpathway of vanillin and vanillate degradation (3/10 steps found)
- L-glutamate degradation VIII (to propanoate) (3/11 steps found)
- syringate degradation (3/12 steps found)
- methylaspartate cycle (8/19 steps found)
- Methanobacterium thermoautotrophicum biosynthetic metabolism (23/56 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
Sequence Analysis Tools
PaperBLAST (search for papers about homologs of this protein)
Search CDD (the Conserved Domains Database, which includes COG and superfam)
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
See A0A346D7I7 at UniProt or InterPro
Protein Sequence (313 amino acids)
>DZA65_RS03130 malate dehydrogenase (Dickeya dianthicola ME23) MKVAVLGAAGGIGQALALLLKTQLPSGSELSLYDIAPVTPGVAVDLSHIPTDVKIKGFSG EDATPALEGADIVLMSAGVARKPGMDRSDLFNVNAGIVRNLVSQIARTCPNACIGIITNP VNTTVAIAAEVLEQAGVYNKDKLFGVTTLDIIRSSTFVAELKDKQPQAIDVPVIGGHSGV TILPLLSRIPGVSFTEQEVADLTKRIQNAGTEVVEAKAGGGSATLSMGQAAARFGLSLVR ALQGESGVVECAYVEGDGKHARFFAQPLLLGKNGVAERKDIGTLSAFEQQALVSMLDTLK QDIALGEEFVNKK