Protein Info for PP_3596 in Pseudomonas putida KT2440
Annotation: D-lysine oxidase
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: K00285, D-amino-acid dehydrogenase [EC: 1.4.99.1] (inferred from 100% identity to ppf:Pput_2176)MetaCyc: 100% identical to D-lysine oxidase (Pseudomonas putida KT2440)
D-amino-acid oxidase. [EC: 1.4.3.3]
Predicted SEED Role
"D-amino acid dehydrogenase small subunit (EC 1.4.99.1)" in subsystem Pyruvate Alanine Serine Interconversions or Respiratory dehydrogenases 1 (EC 1.4.99.1)
MetaCyc Pathways
- L-lysine degradation V (9/9 steps found)
- superpathway of thiamine diphosphate biosynthesis II (8/11 steps found)
- thiazole component of thiamine diphosphate biosynthesis II (4/7 steps found)
- butanol and isobutanol biosynthesis (engineered) (3/8 steps found)
- superpathway of L-lysine degradation (23/43 steps found)
KEGG Metabolic Maps
- Arginine and proline metabolism
- D-Arginine and D-ornithine metabolism
- Glycine, serine and threonine metabolism
- Nitrogen metabolism
- Penicillin and cephalosporin biosynthesis
- Phenylalanine metabolism
Isozymes
Compare fitness of predicted isozymes for: 1.4.99.1
Use Curated BLAST to search for 1.4.3.3 or 1.4.99.1
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 Q88GX1 at UniProt or InterPro
Protein Sequence (414 amino acids)
>PP_3596 D-lysine oxidase (Pseudomonas putida KT2440) MHCQTLVLGAGIVGVSTALHLQARGRQVILIDRDEPGSGTSHGNAGLIERSSVIPYAFPR QLSALLRYGLNRQPDVRYSLAHLPKAAPWLWRYWRQSAPGRLAGAAADMLPLVQRCVDEH DALIAAAGLEGLVQAKGWIEVFRDPALFEQAKTDAKGLSRYGLRFEILECGQLQAREHQL DATVVGGIHWLDPKTVNNPGALTRGYAALFLQRGGQFVHGDARSLRQANGQWRVESRRGP ITADEVVACLGPQSADLFSGLGYQIPLAIKRGYHMHYSTRDGAQLEHSICDTQGGYVLAP MARGVRLTTGIEFDAASAPGNQIQLGRCEALARKLFPALGDRLDDTPWLGRRPCLPDMRP VIGPAPRHPGLWFNFGHAHHGLTLGPVCGRLLAELLTGEPPFTDPAPYSATRFD