RegulonDB

Gene
Name:	ldtC
Synonym(s):	ECK1099, G6571, b1113, ycfS
Genome position(nucleotides):	1169412 <-- 1170374 Genome Browser
Strand:	reverse
Sequence:	Get nucleotide sequence FastaFormat
GC content %:	53.27
External database links:

ASAP:	ABE-0003760
ECHOBASE:	EB3211
OU-MICROARRAY:	b1113
PortEco:	ycfS
STRING:	511145.b1113
COLOMBOS:	ldtC

Gene

Name:

ldtC

Synonym(s):

ECK1099, G6571, b1113, ycfS

Genome position(nucleotides):

1169412 <-- 1170374 Genome Browser

Strand:

reverse

Sequence:

Get nucleotide sequence FastaFormat

GC content %:

53.27

External database links:

ASAP:

ECHOBASE:

OU-MICROARRAY:

PortEco:

STRING:

COLOMBOS:

Type

Positions

Sequence

1 -> 23

MMIKTRFSRWLTFFTFAAAVALA

103 -> 240

GIVINIAELRLYYYPPGKNSVTVYPIGIGQLGGDTLTPTMVTTVSDKRANPTWTPTANIRARYKAQGIELPAVVPAGLDNPMGHHAIRLAAYGGVYLLHGTNADFGIGMRVSSGCIRLRDDDIKTLFSQVTPGTKVNI

45 -> 90

KFHVVENDGGSLEAIAKKYNVGFLALLQANPGVDPYVPRAGSVLTI

47 -> 91

HVVENDGGSLEAIAKKYNVGFLALLQANPGVDPYVPRAGSVLTIP

244 -> 310

PIKVSAEPNGARLVEVHQPLSEKIDDDPQLLPITLNSAMQSFKDAAQTDAEVMQHVMDVRSGMPVDV

Type

Positions

Sequence

1 -> 23

MMIKTRFSRWLTFFTFAAAVALA

103 -> 240

GIVINIAELRLYYYPPGKNSVTVYPIGIGQLGGDTLTPTMVTTVSDKRANPTWTPTANIRARYKAQGIELPAVVPAGLDNPMGHHAIRLAAYGGVYLLHGTNADFGIGMRVSSGCIRLRDDDIKTLFSQVTPGTKVNI

45 -> 90

KFHVVENDGGSLEAIAKKYNVGFLALLQANPGVDPYVPRAGSVLTI

47 -> 91

HVVENDGGSLEAIAKKYNVGFLALLQANPGVDPYVPRAGSVLTIP

244 -> 310

PIKVSAEPNGARLVEVHQPLSEKIDDDPQLLPITLNSAMQSFKDAAQTDAEVMQHVMDVRSGMPVDV

24 -> 320

LPAKANTWPLPPAGSRLVGENKFHVVENDGGSLEAIAKKYNVGFLALLQANPGVDPYVPRAGSVLTIPLQTLLPDAPREGIVINIAELRLYYYPPGKNSVTVYPIGIGQLGGDTLTPTMVTTVSDKRANPTWTPTANIRARYKAQGIELPAVVPAGLDNPMGHHAIRLAAYGGVYLLHGTNADFGIGMRVSSGCIRLRDDDIKTLFSQVTPGTKVNIINTPIKVSAEPNGARLVEVHQPLSEKIDDDPQLLPITLNSAMQSFKDAAQTDAEVMQHVMDVRSGMPVDVRRHQVSPQTL

201 -> 220

HGTNADFGIGMRVSSGCIRL

Multifun Terms (GenProtEC)

1 - metabolism --> 1.6 - biosynthesis of macromolecules (cellular constituents) --> 1.6.7 - murein (peptidoglycan)

Gene Ontology Terms (GO)

cellular_component

GO:0030288 - outer membrane-bounded periplasmic space
GO:0042597 - periplasmic space

molecular_function

GO:0016757 - transferase activity, transferring glycosyl groups
GO:0016787 - hydrolase activity
GO:0016740 - transferase activity
GO:0004180 - carboxypeptidase activity
GO:0071972 - peptidoglycan L,D-transpeptidase activity

biological_process

GO:0006508 - proteolysis
GO:0009252 - peptidoglycan biosynthetic process
GO:0008360 - regulation of cell shape
GO:0018104 - peptidoglycan-protein cross-linking
GO:0071555 - cell wall organization

Transcriptional Regulation
	Display Regulation
Activated by:	CpxR

Transcriptional Regulation

Display Regulation

Activated by:

CpxR

	Type	Name	Post Left	Post Right	Strand	Notes	Evidence (Confirmed, Strong, Weak)	References
	promoter	TSS_1443	1171800		reverse	nd	[RS-EPT-CBR]	[3]
	promoter	TSS_1444 (cluster)	1173832		reverse	For this promoter, there is a cluster of 2 transcription start sites,in the interval 1173831 to 1173832, where the highest frequency is at position 1173055. The most upstream position of this cluster is assigned as TSS position in the promoter. Read more >	[RS-EPT-CBR]	[3]

Type

Name

Post Left

Post Right

Strand

Notes

Evidence (Confirmed, Strong, Weak)

References

promoter

TSS_1443

1171800

reverse

[RS-EPT-CBR]

[3]

promoter

TSS_1444 (cluster)

1173832

reverse

For this promoter, there
Read more >

[RS-EPT-CBR]

[3]

Evidence
[RS-EPT-CBR] RNA-seq using two enrichment strategies for primary transcripts and consistent biological replicates

Evidence

[RS-EPT-CBR] RNA-seq using two enrichment strategies for primary transcripts and consistent biological replicates

Reference(s)
[1] Egler M., Grosse C., Grass G., Nies DH., 2005, Role of the extracytoplasmic function protein family sigma factor RpoE in metal resistance of Escherichia coli., J Bacteriol 187(7):2297-307
[2] Kuru E., Radkov A., Meng X., Egan A., Alvarez L., Dowson A., Booher G., Breukink E., Roper DI., Cava F., Vollmer W., Brun Y., VanNieuwenhze MS., 2019, Mechanisms of Incorporation for D-Amino Acid Probes That Target Peptidoglycan Biosynthesis., ACS Chem Biol 14(12):2745-2756
[3] 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.

Reference(s)

[1] Egler M., Grosse C., Grass G., Nies DH., 2005, Role of the extracytoplasmic function protein family sigma factor RpoE in metal resistance of Escherichia coli., J Bacteriol 187(7):2297-307

[2] Kuru E., Radkov A., Meng X., Egan A., Alvarez L., Dowson A., Booher G., Breukink E., Roper DI., Cava F., Vollmer W., Brun Y., VanNieuwenhze MS., 2019, Mechanisms of Incorporation for D-Amino Acid Probes That Target Peptidoglycan Biosynthesis., ACS Chem Biol 14(12):2745-2756

[3] 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.