Detailed information of TA system TA006332

Experimentally validated

Overview

TA module

• Type: I
• Classification (family/domain): ldrD-rdlD/-
• Location: 3699980..3700201
• Replicon: chromosome
• Accession: NC_000913
• Organism: Escherichia coli str. K-12 substr. MG1655
• T1TAdb ID: TA06181

Toxin (Protein)

• Gene name: ldrD
• Uniprot ID: Q6BF25
• Locus tag: b4453
• Protein ID: YP_026227.1
• Coordinates: 3699980..3700087 (-)
• Length: 36 a.a.

Antitoxin (RNA)

Gene name	rdlD
Locus tag	b4454
Coordinates	3700135..3700201 (+)

Genomic Context

Locus tag	Coordinates	Strand	Size (bp)	Protein ID	Product	Description
b3535	3695997..3696185	-	189	NP_417992.1	PF10945 family protein YhjR	-
b3536	3696458..3698029	+	1572	NP_417993.1	c-di-GMP-binding protein BcsE	-
b3537	3698026..3698217	+	192	NP_417994.2	putative cellulose biosynthesis protein BcsF	-
b3538	3698214..3699893	+	1680	NP_417995.1	cellulose phosphoethanolamine transferase	-
b4453	3699980..3700087	-	108	YP_026227.1	small toxic polypeptide LdrD	Toxin
-	3700135..3700201	+	67	-	-	Antitoxin
b3539	3700563..3701834	+	1272	NP_417996.1	putative transporter YhjV	-
b3540	3701864..3702868	-	1005	NP_417997.1	dipeptide ABC transporter ATP binding subunit DppF	-
b3541	3702865..3703848	-	984	NP_417998.1	dipeptide ABC transporter ATP binding subunit DppD	-
b3542	3703859..3704761	-	903	NP_417999.1	dipeptide ABC transporter membrane subunit DppC	-

Associated MGEs

MGE detail	Similar MGEs	Relative position	MGE Type	Cargo ARG	Virulence gene	Coordinates	Length (bp)

Relative position:
(1) inside: TA loci is completely located inside the MGE;
(2) overlap: TA loci is partially overlapped with the MGE;
(3) flank: The TA loci is located in the 5 kb flanking regions of MGE.

Domains

Predicted by InterproScan

Toxin

• Type I toxin-antitoxin system, toxin Ldr (1-35)

Sequences

Toxin

Protein

• Length: 36 a.a.
• Molecular weight: 3916.72 Da
• Isoelectric Point: 9.0157

>T6332 YP_026227.1 NC_000913:c3700087-3699980 [Escherichia coli str. K-12 substr. MG1655]
MTFAELGMAFWHDLAAPVIAGILASMIVNWLNKRK

Nucleotide

• Length: 108 bp

>T6332 NC_000913:c3700087-3699980 [Escherichia coli str. K-12 substr. MG1655]
ATGACGTTCGCAGAGCTGGGCATGGCCTTCTGGCATGATTTAGCGGCTCCGGTCATTGCTGGCATTCTTGCCAGTATGAT
CGTGAACTGGCTGAACAAGCGGAAGTAA

Antitoxin

Nucleotide

• Length: 67 bp

>AT6332 NC_000913:3700135-3700201 [Escherichia coli str. K-12 substr. MG1655]
GGTCTAGAGTCAAGATTAGCCCCCGTGGTGTTGTCAGGTGCATACCTGCAACGTGCGGGGGTTTTCT

Similar Proteins

Only experimentally validated proteins are listed.

Toxin

Protein	Organism	Identities (%)	Coverage (%)	Ha-value
T6348	Escherichia coli K-12 strain ER3413	100	100	1
T6340	Escherichia coli str. K-12 substr. MDS42	100	100	1
T6344	Escherichia coli str. K-12 substr. W3110	100	100	1
T6336	Escherichia coli str. K-12 substr. DH10B	100	100	1
T6328	Escherichia coli str. K-12 substr. MC4100	100	100	1
T6347	Escherichia coli K-12 strain ER3413	57.143	100	0.571
T6345	Escherichia coli K-12 strain ER3413	57.143	100	0.571
T6339	Escherichia coli str. K-12 substr. MDS42	57.143	100	0.571
T6337	Escherichia coli str. K-12 substr. MDS42	57.143	100	0.571
T6335	Escherichia coli str. K-12 substr. DH10B	57.143	100	0.571
T6333	Escherichia coli str. K-12 substr. DH10B	57.143	100	0.571
T6343	Escherichia coli str. K-12 substr. W3110	57.143	100	0.571
T6341	Escherichia coli str. K-12 substr. W3110	57.143	100	0.571
T6331	Escherichia coli str. K-12 substr. MG1655	57.143	100	0.571
T6329	Escherichia coli str. K-12 substr. MG1655	57.143	100	0.571
T6342	Escherichia coli str. K-12 substr. W3110	57.143	100	0.571
T6334	Escherichia coli str. K-12 substr. DH10B	57.143	100	0.571
T6338	Escherichia coli str. K-12 substr. MDS42	57.143	100	0.571
T6346	Escherichia coli K-12 strain ER3413	57.143	100	0.571
T6325	Escherichia coli str. K-12 substr. MC4100	57.143	100	0.571
T6326	Escherichia coli str. K-12 substr. MC4100	57.143	100	0.571
T6327	Escherichia coli str. K-12 substr. MC4100	57.143	100	0.571
T6330	Escherichia coli str. K-12 substr. MG1655	57.143	100	0.571

Multiple sequence alignment

Structures

Toxin

• PDB: 5LBJ

Antitoxin

References

(1) Mitsuoki Kawano et al. (2002) Molecular characterization of long direct repeat (LDR) sequences expressing a stable mRNA encoding for a 35-amino-acid cell-killing peptide and a cis-encoded small antisense RNA in Escherichia coli. Molecular Microbiology 45(2):333-49. [PubMed:12123448]

(2) Elizabeth M Fozo et al. (2010) Abundance of type I toxin-antitoxin systems in bacteria: searches for new candidates and discovery of novel families. Nucleic Acids Research 38(11):3743-59. [PubMed:20156992]


 experimental literature