Protein Info for PP_1339 in Pseudomonas putida KT2440

Annotation: D-alanine--D-alanine ligase B

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

• PF01820: Dala_Dala_lig_N
  • amino acids 19 to 58 (40 residues), 36.5 bits, 2.3e-12
  • amino acids 66 to 101 (36 residues), 42.8 bits, 2.5e-14
• TIGR01205: D-alanine--D-alanine ligase
  • amino acids 19 to 312 (294 residues), 354 bits, E=3.1e-110
• PF02655: ATP-grasp_3
  • amino acids 110 to 281 (172 residues), 25.2 bits, E=5.6e-09
• PF02786: CPSase_L_D2
  • amino acids 111 to 282 (172 residues), 41 bits, E=5.6e-14
• PF02222: ATP-grasp
  • amino acids 118 to 197 (80 residues), 34.9 bits, E=4.3e-12
• PF07478: Dala_Dala_lig_C
  • amino acids 118 to 310 (193 residues), 191.5 bits, E=4.6e-60
• PF13535: ATP-grasp_4
  • amino acids 146 to 281 (136 residues), 31.3 bits, E=5.3e-11

Best Hits

Swiss-Prot: 100% identical to DDLB_PSEPK: D-alanine--D-alanine ligase B (ddlB) from Pseudomonas putida (strain ATCC 47054 / DSM 6125 / NCIMB 11950 / KT2440)

KEGG orthology group: K01921, D-alanine-D-alanine ligase [EC: 6.3.2.4] (inferred from 100% identity to ppu:PP_1339)

Predicted SEED Role

"D-alanine--D-alanine ligase (EC 6.3.2.4)" in subsystem Peptidoglycan Biosynthesis (EC 6.3.2.4)

MetaCyc Pathways

• peptidoglycan biosynthesis I (meso-diaminopimelate containing) (12/12 steps found)
• UDP-N-acetylmuramoyl-pentapeptide biosynthesis I (meso-diaminopimelate containing) (8/8 steps found)
• UDP-N-acetylmuramoyl-pentapeptide biosynthesis II (lysine-containing) (7/8 steps found)
• UDP-N-acetylmuramoyl-pentapeptide biosynthesis III (meso-diaminopimelate containing) (6/8 steps found)
• peptidoglycan biosynthesis III (mycobacteria) (11/15 steps found)
• peptidoglycan biosynthesis II (staphylococci) (12/17 steps found)
• peptidoglycan biosynthesis IV (Enterococcus faecium) (12/17 steps found)
• peptidoglycan biosynthesis V (β-lactam resistance) (11/17 steps found)

KEGG Metabolic Maps

• D-Alanine metabolism
• Peptidoglycan biosynthesis

Isozymes

Compare fitness of predicted isozymes for: 6.3.2.4

Use Curated BLAST to search for 6.3.2.4

Sequence Analysis Tools

See Q88N74 at UniProt or InterPro

Protein Sequence (318 amino acids)

>PP_1339 D-alanine--D-alanine ligase B (Pseudomonas putida KT2440)
MTSAYDKLHSTLDVKAFGRVAVLYGGKSAEREVSLKSGAAVIDALSTAGVDVVAIDVGDD
LLARLQSEKIDRAFIILHGRGGEDGSMQGLLECLGIPYTGSGILASALAMDKLRTKQVWQ
SLGIPTPRHAVLASESDCLQASTELGFPLIVKPAHEGSSIGMAKVNSTQELVAAWQDAAK
YDSQVLVEQWIHGPEFTIAVLRGQVLPPIALGTPHVFYDYDAKYIVNDTQYRIPCGLDSV
KEQELIDLTARACDAIGIEGWGRLDVMQDEQGRFWLLEVNTAPGMTDHSLVPMAARAAGL
DFQQLVLAILAESVATRG