RegulonDB

Gene
Name:	ldcA
Synonym(s):	ECK1180, G6621, b1192, ycgQ
Genome position(nucleotides):	1242166 <-- 1243080 Genome Browser
Strand:	reverse
Sequence:	Get nucleotide sequence FastaFormat
GC content %:	53.01
External database links:

ASAP:	ABE-0004002
ECHOBASE:	EB3657
ECOO157CYC:	Z1955
OU-MICROARRAY:	b1192
PortEco:	ldcA
STRING:	511145.b1192
COLOMBOS:	ldcA

Product

Name:

murein L,D-carboxypeptidase

Synonym(s):

LdcA, YcgQ

Sequence:

Get amino acid sequence Fasta Format

Cellular location:

cytosol

Molecular weight:

33.567

Isoelectric point:

6.576

Motif(s):

Type	Positions	Sequence
	5 -> 126	HLIAPSGYCIKQHAALRGIQRLTDAGHQVNNVEVIARRCERFAGTETERLEDLNSLARLTTPNTIVLAVRGGYGASRLLADIDWQALVARQQHDPLLICGHSDFTAIQCGLLAHGNVITFSG
	169 -> 283	EGTLWGGNLAMLISLIGTPWMPKIENGILVLEDINEHPFRVERMLLQLYHAGILPRQKAIILGSFSGSTPNDYDAGYNLESVYAFLRSRLSIPLITGLDFGHEQRTVTLPLGAHA

Classification:

Multifun Terms (GenProtEC)
		1 - metabolism --> 1.2 - degradation of macromolecules --> 1.2.3 - proteins/peptides/glycopeptides
		1 - metabolism --> 1.7 - central intermediary metabolism --> 1.7.34 - murein turnover, recycling
		6 - cell structure --> 6.2 - murein
Gene Ontology Terms (GO)
	cellular_component	GO:0005737 - cytoplasm GO:0005829 - cytosol
	molecular_function	GO:0008233 - peptidase activity GO:0016787 - hydrolase activity GO:0004180 - carboxypeptidase activity GO:0008236 - serine-type peptidase activity
	biological_process	GO:0006508 - proteolysis GO:0009050 - glycopeptide catabolic process GO:0009252 - peptidoglycan biosynthetic process GO:0009254 - peptidoglycan turnover GO:0008360 - regulation of cell shape GO:0071555 - cell wall organization

Note(s):

Note(s): ...[more].

Reference(s):

[1] Beck BD., et al., 1977
[2] Beck BD., et al., 1976
[3] Metz R., et al., 1986
[4] Metz R., et al., 1986

External database links:

DIP:

ECOCYC:

ECOLIWIKI:

ECOO157CYC:

INTERPRO:

INTERPRO:

INTERPRO:

INTERPRO:

INTERPRO:

INTERPRO:

PANTHER:

PDB:

PDB:

PFAM:

PFAM:

PRIDE:

PRODB:

REFSEQ:

SMR:

UNIPROT:

Operon

Name:

ldcA

Operon arrangement:

Transcription unit	Promoter

Elements in the selected gene context region unrelated to any object in RegulonDB

Type	Name	Post Left	Strand	Notes	Evidence (Confirmed, Strong, Weak)	References
promoter	TSS_1517	1242102	reverse	nd	[RS-EPT-CBR]	[5]
promoter	cvrAp6	1242164	reverse	Similarity to the consensus sequence of the set of known functional promoters for this sigma factor with strong experimental evidence: high homology. Score: 4.864. P-value: 5.342e-6 Read more >	[ICWHO]	[6]
promoter	TSS_1518 (cluster)	1243112	reverse	For this promoter, there is a cluster of 2 transcription start sites,in the interval 1243111 to 1243112, where the highest frequency is at position 1242334. The most upstream position of this cluster is assigned as TSS position in the promoter. Read more >	[RS-EPT-CBR]	[5]
promoter	emtAp4	1243125	forward	Similarity to the consensus sequence of the set of known functional promoters for this sigma factor with strong experimental evidence: good homology. Score: 3.84. P-value: 8.356e-5 Read more >	[ICWHO]	[6]
promoter	TSS_1519	1243161	reverse	nd	[RS-EPT-CBR]	[5]
promoter	ldcAp9	1243197	reverse	Similarity to the consensus sequence of the set of known functional promoters for this sigma factor with strong experimental evidence: high homology. Score: 9.705. P-value: 1.228e-6 Read more >	[ICWHO]	[6]
promoter	TSS_1520	1243371	forward	nd	[RS-EPT-CBR]	[5]

Evidence
[RS-EPT-CBR] RNA-seq using two enrichment strategies for primary transcripts and consistent biological replicates
[ICWHO] Inferred computationally without human oversight

Reference(s)
[1] Beck BD., Park JT., 1977, Basis for the observed fluctuation of carboxypeptidase II activity during the cell cycle in BUG 6, a temperature-sensitive division mutant of Escherichia coli., J Bacteriol 130(3):1292-302
[2] Beck BD., Park JT., 1976, Activity of three murein hydrolases during the cell division cycle of Escherichia coli K-12 as measured in toluene-treated cells., J Bacteriol 126(3):1250-60
[3] Metz R., Henning S., Hammes WP., 1986, LD-carboxypeptidase activity in Escherichia coli. I. The LD-carboxypeptidase activity in ether treated cells., Arch Microbiol 144(2):175-80
[4] Metz R., Henning S., Hammes WP., 1986, LD-carboxypeptidase activity in Escherichia coli. II. Isolation, purification and characterization of the enzyme from E. coli K 12., Arch Microbiol 144(2):181-6
[5] Salgado H, Peralta-Gil M, Gama-Castro S, Santos-Zavaleta A, Muñiz-Rascado L, García-Sotelo JS, Weiss V, Solano-Lira H, Martínez-Flores I, Medina-Rivera A, Salgado-Osorio G, Alquicira-Hernández S, Alquicira-Hernández K, López-Fuentes A, Porrón-Sotelo L, Huerta AM, Bonavides-Martínez C, Balderas-Martínez YI, Pannier L, Olvera M, Labastida A, Jiménez-Jacinto V, Vega-Alvarado L, Del Moral-Chávez V, Hernández-Alvarez A, Morett E, Collado-Vides J., 2012, RegulonDB v8.0: omics data sets, evolutionary conservation, regulatory phrases, cross-validated gold standards and more., Nucleic Acids Res.
[6] Huerta AM., Collado-Vides J., 2003, Sigma70 promoters in Escherichia coli: specific transcription in dense regions of overlapping promoter-like signals., J Mol Biol 333(2):261-78