Protein Info for PP_4493 in Pseudomonas putida KT2440
Updated annotation (from data): D-2-hydroxyglutarate dehydrogenase (EC 1.1.99.39)
Rationale: Specifically important in carbon source D-Lysine; carbon source L-Lysine; carbon source DL-2-Aminoadipic acid. This is part of the pathway from D-lysine to 2-oxoglutarate. For detailed rationale, see PMC6509195.
Original annotation: putative oxidoreductase
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
KEGG orthology group: K06911, (no description) (inferred from 96% identity to ppw:PputW619_3782)MetaCyc: 100% identical to (R)-2-hydroxyglutarate dehydrogenase (Pseudomonas putida KT2440)
RXN-14932 [EC: 1.1.99.39]
Predicted SEED Role
"Glycolate dehydrogenase (EC 1.1.99.14), subunit GlcD" in subsystem Glycolate, glyoxylate interconversions or Photorespiration (oxidative C2 cycle) (EC 1.1.99.14)
MetaCyc Pathways
- L-lysine degradation V (9/9 steps found)
- glycolate and glyoxylate degradation I (4/4 steps found)
- superpathway of glycol metabolism and degradation (6/7 steps found)
- glycolate and glyoxylate degradation II (2/2 steps found)
- photorespiration II (7/10 steps found)
- photorespiration I (6/9 steps found)
- photorespiration III (6/9 steps found)
- glycolate and glyoxylate degradation III (1/3 steps found)
- superpathway of L-lysine degradation (23/43 steps found)
KEGG Metabolic Maps
Isozymes
Compare fitness of predicted isozymes for: 1.1.99.14
Use Curated BLAST to search for 1.1.99.14 or 1.1.99.39
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 Q88EH0 at UniProt or InterPro
Protein Sequence (1006 amino acids)
>PP_4493 D-2-hydroxyglutarate dehydrogenase (EC 1.1.99.39) (Pseudomonas putida KT2440) MIAQLSTVAPSANYPEFLEALRNSGFRGQISADYATRTVLATDNSIYQRLPQAAVFPLDA DDVARVATLMGEPRFQQVKLTPRGGGTGTNGQSLTDGIVVDLSRHMNNILEINVEERWVR VQAGTVKDQLNAALKPHGLFFAPELSTSNRATVGGMINTDASGQGSCTYGKTRDHVLELH SVLLGGERLHSLPIDDAALEQACAAPGRVGEVYRMAREIQETQAELIETTFPKLNRCLTG YDLAHLRDEQGRFNLNSVLCGAEGSLGYVVEAKLNVLPIPKYAVLVNVRYTSFMDALRDA NALMAHKPLSIETVDSKVLMLAMKDIVWHSVAEYFPADPERPTLGINLVEFCGDEPAEVN AKVQAFIQHLQSDTSVERLGHTLAEGAEAVTRVYTMRKRSVGLLGNVEGEVRPQPFVEDT AVPPEQLADYIADFRALLDGYGLAYGMFGHVDAGVLHVRPALDMKDPVQAALVKPISDAV AALTKRYGGLLWGEHGKGLRSEYVPEYFGELYPALQRLKGAFDPHNQLNPGKICTPLGSA EGLTPVDGVTLRGDLDRTIDERVWQDFPSAVHCNGNGACYNYDPNDAMCPSWKATRERQH SPKGRASLMREWLRLQGEANIDVLAAARNKVSWLKGLPARLRNNRARNQGQEDFSHEVYD AMAGCLACKSCAGQCPIKVNVPDFRSRFLELYHGRYQRPLRDYLIGSLEFTIPYLAHAPG LYNAVMGSKWVSQLLADKVGMVDSPLISRFNFQATLTRCRVGMATVPALRELTPAQRERS IVLVQDAFTRYFETPLLSAFIDLAHRLGHRVFLAPYSANGKPLHVQGFLGAFAKAAIRNA TQLKALADCGVPLVGLDPAMTLVYRQEYQKVPGLEGCPKVLLPQEWLMDVLPEQAPAAPG SFRLMAHCTEKTNVPASTRQWEQVFARLGLKLVTEATGCCGMSGTYGHEARNQETSRTIF EQSWATKLDKDGEPLATGYSCRSQVKRMTERKMRHPLEVVLQYAQR