Combrex Enter Keyword, gene symbol, or identifier (more options; Help )
Enter species name
Gene functional status (select)
Phenotype association (select)[View list of phenotypes]
Check to restrict search to:
Genes in Category A-C and Emerging/Re-Emerging pathogens
Genes in curated Protein Clusters
Genes with predictions submitted to COMBREX
Genes with solved structures in PDB
Genes with Pfam domains shared with human proteins
Genes with products purified by PSI
Genes cloned by PSI
close options


Gene ddlA from Escherichia coli str. K-12 substr. MG1655: D-alanine-D-alanine ligase A
Member of NCBI Protein Clusters PRK01966(See COMBREX Page ) (See NCBI page)
NCBI Entrez GeneID 945313
UniProtKB accession
RefSeq Protein accession NP_414915.1 (PROVISIONAL)
Gene Symbol(s)
  • symbol: ddlA
  • locus tag: b0381
  • aliases: ECK0376, JW0372
Organism Escherichia coli str. K-12 substr. MG1655 (NCBI TaxID: 511145)
Other Cross References:
  • S
    Structure(s) available in PDB:
  • C
    Gene cloned by a participant in the Protein Structure Initiative (PSI): TargetDB. (To obtain a clone, please contact the PSI:Biology-Materials Repository.)
  • U
    Protein purified by a participant in the Protein Structure Initiative (PSI): TargetDB. (If you are interested in collaborating to obtain the protein, please contact the Northeast Structural Genomics consortium).
  • Protein described in EcoCyc: EG10213
Initiate the grant application process for experimentally validating this gene (Important notice about COMBREX grants.)
Contribute a predicted function for this gene (free text, GO terms, or EC number) (info). Be sure to check the list of current predicted functions in the section immediately below beforehand.
Nominate this gene for the Gold Standard Gene Database (if you believe it has been experimentally validated) (info).
Post a comment about this gene to appear on this page (info).
Source Predicted function(s)
NCBI Protein Cluster Prediction D-alanyl-alanine synthetase A
COMBREX ddl D-alanine--D-alanine ligase A (source organism: Salmonella enterica subsp. enterica serovar Typhimurium; strain specific ID: NCBI_TaxID=90371) [More information on this prediction]
Source References Functional description
GSDB Under Review D-alanine--D-alanine ligase A (source organism: Escherichia coli K12; strain specific ID: NCBI_TaxID=83333)
Functional Status greenGreen (experimental evidence, uncurated)
EC number
GO terms
  • MF: GO:0003824 : catalytic activity : IEA
  • MF: GO:0046872 : metal ion binding : IEA
  • CC: GO:0005618 : cell wall : IEA
  • MF: GO:0005524 : ATP binding : IEA
  • MF: GO:0016874 : ligase activity : IEA
  • MF: GO:0030145 : manganese ion binding : IEA
  • MF: GO:0008716 : D-alanine-D-alanine ligase activity : IEA
  • BP: GO:0009252 : peptidoglycan biosynthetic process : IEA
  • BP: GO:0008360 : regulation of cell shape : IEA
  • MF: GO:0000166 : nucleotide binding : IEA
  • MF: GO:0000287 : magnesium ion binding : IEA
  • CC: GO:0005737 : cytoplasm : IEA
  • BP: GO:0007047 : cellular cell wall organization : IEA
Domain Structure from CDD
  • ddl: D-alanyl-alanine synthetase A; Reviewed
  • Dala_Dala_lig_N: D-ala D-ala ligase N-terminus. This family represents the N-terminal region of the D-alanine--D-alanine ligase enzyme EC.... (More)
  • CPSase_L_D2: Carbamoyl-phosphate synthase L chain, ATP binding domain. Members of this protein family contain a region of homology to.... (More)

See domain structure on NCBI Conserved Domain Database
Domain structure from Pfam
See domain structure on Pfam Database
Based on the function of this gene, COMBREX predictions were made to the following related genes (mouse over gene symbol for details) [Download ]
ddl (45) , ddlA (3)
The table at right lists genes that may be "functionally linked to" (i.e., participate in a common biological process, or form a protein complex with) the subject gene of this page, as determined by two sequence-independent methods, including phylogenetic profiling and operon membership (determined by OperonDB). (Info.) These linkages may also be viewed graphically using the program VisANT, by clicking on the headers of the table. Note: VisANT requires Java. To install the latest version of Java, see
 phylogenetic profile
domain fusion
recGATP-dependent DNA helicase
torRDNA-binding response regulator in two-component re
rluF23S rRNA U2604 pseudouridine synthase
polAfused DNA polymerase I 5'->3' polymerase/3'->5' ex
yedWpredicted DNA-binding response regulator in two-co
murBUDP-N-acetylenolpyruvoylglucosamine reductase, FAD
priAPrimosome factor n' (replication factor Y)
murCUDP-N-acetylmuramate:L-alanine ligase
clpPproteolytic subunit of ClpA-ClpP and ClpX-ClpP ATP
phoPDNA-binding response regulator in two-component re
arcADNA-binding response regulator in two-component re
creBDNA-binding response regulator in two-component re
cpxRDNA-binding response regulator in two-component re
radADNA repair protein
clpXATPase and specificity subunit of ClpX-ClpP ATP-de
murAUDP-N-acetylglucosamine 1-carboxyvinyltransferase
rsuA16S rRNA U516 pseudouridine synthase
mrdBcell wall shape-determining protein
rstAmulticopy supressor of yjeE, yeaZ or ygjD deletion
cusRDNA-binding response regulator in two-component re
ftsItranspeptidase involved in septal peptidoglycan sy
mfdtranscription-repair coupling factor
baeRDNA-binding response regulator in two-component re
ftsWintegral membrane protein involved in stabilizing
rluE23S rRNA U2457 pseudouridine synthase
qseBquorum sensing DNA-binding response regulator in t
kdpEDNA-binding response regulator in two-component re
rluB23S rRNA pseudouridylate synthase
basRDNA-binding response regulator in two-component re
mrdAtranspeptidase involved in peptidoglycan synthesis
murGN-acetylglucosaminyl transferase
phoBDNA-binding response regulator in two-component re
ompRDNA-binding response regulator in two-component re
Metabolic Annotation from Palsson Lab

Metabolic Reaction: ALAALAr

D-alanine-D-alanine ligase (reversible)
2 ala-DASH-D[c] + atp[c] <=> adp[c] + alaala[c] + h[c] + pi[c]
Cell Envelope Biosynthesis
Other Genes

Source: Ported to COMBREX by Segre's Lab