Protein Info for PGA1_c11910 in Phaeobacter inhibens DSM 17395
Updated annotation (from data): Malate dehydrogenase (decarboxylating) (EC 1.1.1.39)
Rationale: Specifically important for utilizing L-Malic acid disodium salt monohydrate. Automated validation from mutant phenotype: the predicted function (1.1.1.39-RXN) was linked to the condition via a MetaCyc pathway. This annotation was also checked manually.
Original annotation: NAD-dependent malic enzyme
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: 58% identical to MAO1_RHIME: NAD-dependent malic enzyme (dme) from Rhizobium meliloti (strain 1021)
KEGG orthology group: K00029, malate dehydrogenase (oxaloacetate-decarboxylating)(NADP+) [EC: 1.1.1.40] (inferred from 86% identity to sit:TM1040_1573)Predicted SEED Role
"NADP-dependent malic enzyme (EC 1.1.1.40)" in subsystem Pyruvate metabolism I: anaplerotic reactions, PEP (EC 1.1.1.40)
MetaCyc Pathways
- gluconeogenesis I (12/13 steps found)
- C4 photosynthetic carbon assimilation cycle, NADP-ME type (4/7 steps found)
- methylgallate degradation (2/6 steps found)
- protocatechuate degradation I (meta-cleavage pathway) (3/8 steps found)
- C4 photosynthetic carbon assimilation cycle, PEPCK type (7/14 steps found)
- superpathway of vanillin and vanillate degradation (3/10 steps found)
- syringate degradation (3/12 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 terpenoids and steroids
- Carbon fixation in photosynthetic organisms
- Pyruvate metabolism
Isozymes
Compare fitness of predicted isozymes for: 1.1.1.40
Use Curated BLAST to search for 1.1.1.39 or 1.1.1.40
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 I7DZM6 at UniProt or InterPro
Protein Sequence (762 amino acids)
>PGA1_c11910 Malate dehydrogenase (decarboxylating) (EC 1.1.1.39) (Phaeobacter inhibens DSM 17395) MTKNPKSDTQTLRDAALHYHAYPNPGKLEIRATKPMANGRDLARAYSPGVAEACLEIKSD PADAAKYTSRGNLVAVVTNGTAVLGLGNIGALASKPVMEGKAVLFKKFASIDCFDIEVNE SDPEKLADIVCSLEPTFGAINLEDIKAPDCFIVEKICRERMNIPVFHDDQHGTAIVVGAA AKNALHVAGKRFEDIKIVSTGGGAAGIACLNMLVKLGVRRENIWLCDLHGLVYEGRTEDM NPHKSAFAQKTDLRTLDDVIGGADLFLGLSGPNVLKPEMVAKMTDRPIIFALANPNPEIL PDVAREVSPDAIIATGRSDFPNQVNNVLCFPFIFRGALDVGATEINDEMQIACVEGIAEM ARMTTSAEAAAAYQGEQLTFGADYLIPKPFDPRLVGVVSSAVAKAAMESGVAQRPIDDLA AYRAKLNQTVFKSALLMKPVFEAAKAAARRIVFTEGEDERVLRTAQGILEETTETPILIG RPEVIETRCERLGLRIRPGTDFQIVNPENDPRYYDYWTSYHRVMQREGVTPDLAKAIMRT NTTAIGAIMVHRGEADSMICGTFGEYRWHMNYVNQVLGGGTYEPHGALSLVILEDGPLFI GDTHVRIEPTPEQIAQTVIGAARHVRRFGLEPKIALCSQSQFGNTRCDSGARLRAAIGIL DETPRDFIYEGEMNIDTALDPELRARIFPNSRLEGEANVLIFAHADAASGVRNILKMRAG GLEVGPILMGMGNRAHIVSPSITARGLLNMAAIAGTPVTHYS