Protein Info for PP_4346 in Pseudomonas putida KT2440

Annotation: D-alanine--D-alanine ligase A

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

1 50 100 150 200 250 300 352 signal peptide" amino acids 1 to 21 (21 residues), see Phobius details TIGR01205: D-alanine--D-alanine ligase" amino acids 6 to 341 (336 residues), 297.9 bits, see alignment E=3.8e-93 PF01820: Dala_Dala_lig_N" amino acids 6 to 123 (118 residues), 92.6 bits, see alignment E=4e-30 PF02222: ATP-grasp" amino acids 140 to 310 (171 residues), 29.8 bits, see alignment E=6.7e-11 PF07478: Dala_Dala_lig_C" amino acids 141 to 341 (201 residues), 191.5 bits, see alignment E=1.9e-60

Best Hits

Swiss-Prot: 100% identical to DDLA_PSEPK: D-alanine--D-alanine ligase A (ddlA) 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 99% identity to ppf:Pput_1521)

Predicted SEED Role

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

MetaCyc Pathways

KEGG Metabolic Maps

Isozymes

Compare fitness of predicted isozymes for: 6.3.2.4

Use Curated BLAST to search for 6.3.2.4

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 Q88EV6 at UniProt or InterPro

Protein Sequence (352 amino acids)

>PP_4346 D-alanine--D-alanine ligase A (Pseudomonas putida KT2440)
MKQNVIALVFGGRSSEHSVALRSAATIHAALMALGHRVHCVGIDREGNWRYQGEPCQFPG
AVDRSAPLISIRPGHRSLSYTTQESGTVEIGIDLLFPALHGRWGEDGTIQGLAAMCGLPC
VGSGVLGSAMAMDKDVTKRMVQSAGLVVVPWLAMNSMRPWEELVECLGSSTLFVKPATSG
SSIGVSRVSNALEYAAAFAIAAREDTKVLVEAAVCGREIECGVLELEEGLMASVVGEIIK
KEGHAYYDYQAKYDSNSVTGLRVPSLLPPDIVARIQALSVQAFRCLELKGYARVDFFLTE
EGEIILNEINTLPGFTSASMYPKMFECSGYPPPKLVGALVEYGLSSASKERL