Protein Info for PP_5227 in Pseudomonas putida KT2440

Annotation: diaminopimelate decarboxylase

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

• TIGR01048: diaminopimelate decarboxylase
  • amino acids 6 to 410 (405 residues), 527.6 bits, E=8.7e-163
• PF00278: Orn_DAP_Arg_deC
  • amino acids 31 to 368 (338 residues), 94.7 bits, E=4.9e-31
• PF02784: Orn_Arg_deC_N
  • amino acids 35 to 280 (246 residues), 263.1 bits, E=3.5e-82
• PF01168: Ala_racemase_N
  • amino acids 35 to 233 (199 residues), 32.9 bits, E=8.3e-12

Best Hits

Swiss-Prot: 87% identical to DCDA_PSEFL: Diaminopimelate decarboxylase (lysA) from Pseudomonas fluorescens

KEGG orthology group: K01586, diaminopimelate decarboxylase [EC: 4.1.1.20] (inferred from 99% identity to ppg:PputGB1_5288)

Predicted SEED Role

"Diaminopimelate decarboxylase (EC 4.1.1.20)" in subsystem Lysine Biosynthesis DAP Pathway (EC 4.1.1.20)

MetaCyc Pathways

• aspartate superpathway (22/25 steps found)
• superpathway of L-lysine, L-threonine and L-methionine biosynthesis I (16/18 steps found)
• L-lysine biosynthesis I (9/9 steps found)
• superpathway of L-lysine, L-threonine and L-methionine biosynthesis II (13/15 steps found)
• L-lysine biosynthesis III (6/7 steps found)
• L-lysine biosynthesis VI (6/7 steps found)
• L-lysine biosynthesis II (6/9 steps found)

KEGG Metabolic Maps

• Biosynthesis of alkaloids derived from ornithine, lysine and nicotinic acid
• Lysine biosynthesis

Isozymes

Compare fitness of predicted isozymes for: 4.1.1.20

Use Curated BLAST to search for 4.1.1.20

Sequence Analysis Tools

See Q88CF4 at UniProt or InterPro

Protein Sequence (415 amino acids)

>PP_5227 diaminopimelate decarboxylase (Pseudomonas putida KT2440)
MNAFNYRDGELFAEGVALSAIAERYGTPTYVYSRAHIEAQYRSYADALQGTEHLVCFAVK
ANSNLGVLNVLARLGAGFDIVSGGELERVLAAGGRADRVVFSGVGKTREDMRRALEVGVH
CFNVESTDELERLQVVAAEMGKVAPVSLRVNPDVDAGTHPYISTGLKENKFGIAIADAEA
IYVRAAQLPNLEVVGVDCHIGSQLTTVEPFLDALDRLLVLVDRLAECGIHLRHLDLGGGV
GVRYRDEQPPRVADYIKAIRERVGERDLALVFEPGRYIVANAGVLLTRVEYLKHTEHKDF
AIIDAAMNDLIRPALYQAWMGVSAVKPRAGEGRAYDLVGPICETGDFLGKDRVLNLAEGD
LLAVESAGAYGFVMSSNYNTRGRCAEILVDGDQAFEVRRRETVAELYAGESLLPE