Protein Info for PGA1_c29720 in Phaeobacter inhibens DSM 17395
Updated annotation (from data): D-lactate dehydrogenase, FAD-linked subunit GlcD (EC 1.1.99.6)
Rationale: Specifically important for: Sodium D,L-Lactate; Sodium D-Lactate.
Original annotation: glycolate oxidase subunit GlcD
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: 47% identical to GLCD_ECOLI: Glycolate oxidase subunit GlcD (glcD) from Escherichia coli (strain K12)
KEGG orthology group: K00104, glycolate oxidase [EC: 1.1.3.15] (inferred from 90% identity to sit:TM1040_2502)MetaCyc: 47% identical to glycolate dehydrogenase, putative FAD-linked subunit (Escherichia coli K-12 substr. MG1655)
Glycolate dehydrogenase. [EC: 1.1.99.14]; 1.1.99.14 [EC: 1.1.99.14]
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
- glycolate and glyoxylate degradation II (2/2 steps found)
- photorespiration I (7/9 steps found)
- photorespiration III (7/9 steps found)
- photorespiration II (7/10 steps found)
- glycolate and glyoxylate degradation I (2/4 steps found)
- superpathway of glycol metabolism and degradation (4/7 steps found)
- glycolate and glyoxylate degradation III (1/3 steps found)
KEGG Metabolic Maps
Isozymes
Compare fitness of predicted isozymes for: 1.1.99.14, 1.1.99.6
Use Curated BLAST to search for 1.1.3.15 or 1.1.99.14 or 1.1.99.6
Sequence Analysis Tools
PaperBLAST (search for papers about homologs of this protein)
Search CDD (the Conserved Domains Database, which includes COG and superfam)
Compare to protein structures
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 I7EQM9 at UniProt or InterPro
Protein Sequence (482 amino acids)
>PGA1_c29720 D-lactate dehydrogenase, FAD-linked subunit GlcD (EC 1.1.99.6) (Phaeobacter inhibens DSM 17395) MEMPIPDQTVLSQKTELALRLAAVLPDDALVQDPAETRAYECDALTAYKCPPMLVVLPRT TKEVSDVLRICHAAGVPVVPRGAGTSLAGGALPTADCVILGVARMNAVLETDYDNRIIRV QTGRTNLSVSGAVEEEEFFYAPDPSSQLACAIAGNIAMNSGGAHCLKYGVTTNNLMGVTM VMMDGTVVEIGGAHLDAGGLDLLGVICGSEGQLGVVTEATLRILRKPEGARPVLIGYDSN EVAGACVSDIIKAGVLPVAIEFMDRPCIEACEAFAKAGYPMCEALLIVEVEGSDAEIDHQ LRLITEIARSHNPVELREARDSDEAARIWLGRKSAFGAMGQINDYMCLDGTIPVTSLPHV LRRIGEMSKEFGLDVANVFHAGDGNMHPLILFDANKPGDLETCEAFGAEILKLCVEVGGC LTGEHGVGIEKRDLMLDQYGVADIEAQLRVKDVFDPKWLLNPAKVFPLSTTQSRRTPAVT PL