Protein Info for PfGW456L13_3648 in Pseudomonas fluorescens GW456-L13
Updated annotation (from data): D-serine ammonia-lyase (EC 4.3.1.18)
Rationale: Specifically important for utilizing D-Serine. Automated validation from mutant phenotype: the predicted function (4.3.1.18) was linked to the condition via a SEED subsystem. This annotation was also checked manually.
Original annotation: D-serine dehydratase (EC 4.3.1.18)
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: 75% identical to SDHD_PSEMY: Probable D-serine dehydratase (dsdA) from Pseudomonas mendocina (strain ymp)
KEGG orthology group: K01753, D-serine dehydratase [EC: 4.3.1.18] (inferred from 75% identity to pmy:Pmen_3266)MetaCyc: 69% identical to D-serine ammonia-lyase (Escherichia coli K-12 substr. MG1655)
D-serine ammonia-lyase. [EC: 4.3.1.18]
Predicted SEED Role
"D-serine dehydratase (EC 4.3.1.18)" in subsystem Glycine and Serine Utilization or Pyruvate Alanine Serine Interconversions (EC 4.3.1.18)
MetaCyc Pathways
- superpathway of L-lysine, L-threonine and L-methionine biosynthesis II (13/15 steps found)
- glycine betaine degradation III (7/7 steps found)
- D-serine degradation (3/3 steps found)
- L-serine degradation (3/3 steps found)
- L-methionine biosynthesis II (5/6 steps found)
- glycine betaine degradation I (6/8 steps found)
- L-cysteine degradation II (2/3 steps found)
- L-tryptophan degradation II (via pyruvate) (2/3 steps found)
- purine nucleobases degradation II (anaerobic) (16/24 steps found)
- felinine and 3-methyl-3-sulfanylbutan-1-ol biosynthesis (2/5 steps found)
- L-mimosine degradation (4/8 steps found)
- glutathione-mediated detoxification I (3/8 steps found)
KEGG Metabolic Maps
Isozymes
Compare fitness of predicted isozymes for: 4.3.1.18
Use Curated BLAST to search for 4.3.1.18
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 A0A293QQL5 at UniProt or InterPro
Protein Sequence (450 amino acids)
>PfGW456L13_3648 D-serine ammonia-lyase (EC 4.3.1.18) (Pseudomonas fluorescens GW456-L13) MILGKTLESWYASYPLIRDLVALQETTWFNPAVAPVAESIGDVGLTAADVADASARLTRF ASYLRRAFPETECSGGIIESDILPVPHLQQLLGERYGQALQGALWLKRDSHLPISGSIKA RGGIYEVLKHAEDLALAANLLTLDDDYAVLDSDKARAFFGQYKIAVGSTGNLGMSIGIMG AALGFQVTVHMSADARQWKKDKLRSHGVTVIEYSSDYSVAVSQGRQQAESDPACHFVDDE NSVSLFLGYSVAAERLKKQLAAADITVDAQHPLFVYLPCGVGGAPGGVAFGLKLAFGDAV HCIFAEPTHSPCMMLGVYSGLHDEVSVQDFGIDNVTAADGLAVGRASGFVGKAMQRLLDG FYTVSDEEMYSLLALMERSEGVRLEPSALAGVPGIARVQADQQGYLARARLDRQAMVQAT HLVWATGGNMVPCDEMEAYLAKGRELLAKG