Detailed information of TA system TA278960

Bioinformatically predicted

Overview

TA module

• Type: I
• Classification (family/domain): ldrD-rdlD/Ldr(toxin)
• Location: 3671042..3671264
• Replicon: chromosome
• Accession: NZ_CP123365
• Organism: Shigella flexneri strain MMGSG_23

Toxin (Protein)

• Gene name: ldrD
• Uniprot ID: S1NWX0
• Locus tag: PFB08_RS18705
• Protein ID: WP_001295224.1
• Coordinates: 3671042..3671149 (-)
• Length: 36 a.a.

Antitoxin (RNA)

Gene name	rdlD
Locus tag	-
Coordinates	3671198..3671264 (+)

Genomic Context

Locus tag	Coordinates	Strand	Size (bp)	Protein ID	Product	Description
PFB08_RS18675	3666071..3667642	+	1572	WP_001204920.1	cellulose biosynthesis c-di-GMP-binding protein BcsE	-
PFB08_RS18680	3667639..3667830	+	192	WP_000988299.1	cellulose biosynthesis protein BcsF	-
PFB08_RS18685	3667827..3669506	+	1680	WP_000191557.1	cellulose biosynthesis protein BcsG	-
PFB08_RS18690	3669593..3669700	-	108	WP_001295224.1	type I toxin-antitoxin system toxin Ldr family protein	-
-	3669757..3669812	+	56	NuclAT_26	-	-
-	3669757..3669812	+	56	NuclAT_26	-	-
-	3669757..3669812	+	56	NuclAT_26	-	-
-	3669757..3669812	+	56	NuclAT_26	-	-
-	3669757..3669812	+	56	NuclAT_29	-	-
-	3669757..3669812	+	56	NuclAT_29	-	-
-	3669757..3669812	+	56	NuclAT_29	-	-
-	3669757..3669812	+	56	NuclAT_29	-	-
-	3669757..3669812	+	56	NuclAT_32	-	-
-	3669757..3669812	+	56	NuclAT_32	-	-
-	3669757..3669812	+	56	NuclAT_32	-	-
-	3669757..3669812	+	56	NuclAT_32	-	-
-	3669757..3669812	+	56	NuclAT_35	-	-
-	3669757..3669812	+	56	NuclAT_35	-	-
-	3669757..3669812	+	56	NuclAT_35	-	-
-	3669757..3669812	+	56	NuclAT_35	-	-
-	3669757..3669814	+	58	NuclAT_20	-	-
-	3669757..3669814	+	58	NuclAT_20	-	-
-	3669757..3669814	+	58	NuclAT_20	-	-
-	3669757..3669814	+	58	NuclAT_20	-	-
-	3669757..3669814	+	58	NuclAT_23	-	-
-	3669757..3669814	+	58	NuclAT_23	-	-
-	3669757..3669814	+	58	NuclAT_23	-	-
-	3669757..3669814	+	58	NuclAT_23	-	-
PFB08_RS18695	3670076..3670183	-	108	WP_001295224.1	type I toxin-antitoxin system toxin Ldr family protein	-
-	3670240..3670295	+	56	NuclAT_28	-	-
-	3670240..3670295	+	56	NuclAT_28	-	-
-	3670240..3670295	+	56	NuclAT_28	-	-
-	3670240..3670295	+	56	NuclAT_28	-	-
-	3670240..3670295	+	56	NuclAT_31	-	-
-	3670240..3670295	+	56	NuclAT_31	-	-
-	3670240..3670295	+	56	NuclAT_31	-	-
-	3670240..3670295	+	56	NuclAT_31	-	-
-	3670240..3670295	+	56	NuclAT_34	-	-
-	3670240..3670295	+	56	NuclAT_34	-	-
-	3670240..3670295	+	56	NuclAT_34	-	-
-	3670240..3670295	+	56	NuclAT_34	-	-
-	3670240..3670295	+	56	NuclAT_37	-	-
-	3670240..3670295	+	56	NuclAT_37	-	-
-	3670240..3670295	+	56	NuclAT_37	-	-
-	3670240..3670295	+	56	NuclAT_37	-	-
-	3670240..3670297	+	58	NuclAT_22	-	-
-	3670240..3670297	+	58	NuclAT_22	-	-
-	3670240..3670297	+	58	NuclAT_22	-	-
-	3670240..3670297	+	58	NuclAT_22	-	-
-	3670240..3670297	+	58	NuclAT_25	-	-
-	3670240..3670297	+	58	NuclAT_25	-	-
-	3670240..3670297	+	58	NuclAT_25	-	-
-	3670240..3670297	+	58	NuclAT_25	-	-
PFB08_RS18700	3670559..3670666	-	108	WP_000141634.1	type I toxin-antitoxin system toxic polypeptide LdrD	-
-	3670724..3670778	+	55	NuclAT_27	-	-
-	3670724..3670778	+	55	NuclAT_27	-	-
-	3670724..3670778	+	55	NuclAT_27	-	-
-	3670724..3670778	+	55	NuclAT_27	-	-
-	3670724..3670778	+	55	NuclAT_30	-	-
-	3670724..3670778	+	55	NuclAT_30	-	-
-	3670724..3670778	+	55	NuclAT_30	-	-
-	3670724..3670778	+	55	NuclAT_30	-	-
-	3670724..3670778	+	55	NuclAT_33	-	-
-	3670724..3670778	+	55	NuclAT_33	-	-
-	3670724..3670778	+	55	NuclAT_33	-	-
-	3670724..3670778	+	55	NuclAT_33	-	-
-	3670724..3670778	+	55	NuclAT_36	-	-
-	3670724..3670778	+	55	NuclAT_36	-	-
-	3670724..3670778	+	55	NuclAT_36	-	-
-	3670724..3670778	+	55	NuclAT_36	-	-
-	3670724..3670780	+	57	NuclAT_21	-	-
-	3670724..3670780	+	57	NuclAT_21	-	-
-	3670724..3670780	+	57	NuclAT_21	-	-
-	3670724..3670780	+	57	NuclAT_21	-	-
-	3670724..3670780	+	57	NuclAT_24	-	-
-	3670724..3670780	+	57	NuclAT_24	-	-
-	3670724..3670780	+	57	NuclAT_24	-	-
-	3670724..3670780	+	57	NuclAT_24	-	-
PFB08_RS18705	3671042..3671149	-	108	WP_001295224.1	type I toxin-antitoxin system toxin Ldr family protein	Toxin
-	3671198..3671264	+	67	-	-	Antitoxin
PFB08_RS18710	3671625..3672896	+	1272	WP_005052340.1	aromatic amino acid transport family protein	-
PFB08_RS18715	3672926..3673930	-	1005	WP_000107041.1	dipeptide ABC transporter ATP-binding subunit DppF	-
PFB08_RS18720	3673927..3674910	-	984	WP_001196486.1	dipeptide ABC transporter ATP-binding protein	-
PFB08_RS18725	3674921..3675823	-	903	WP_000084666.1	dipeptide ABC transporter permease 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: 3882.70 Da
• Isoelectric Point: 9.0157

>T278960 WP_001295224.1 NZ_CP123365:c3671149-3671042 [Shigella flexneri]
MTLAELGMAFWHDLAAPVIAGILASMIVNWLNKRK

Nucleotide

• Length: 108 bp

Antitoxin

Nucleotide

• Length: 67 bp

>AT278960 NZ_CP123365:3671198-3671264 [Shigella flexneri]
GTCTAGGTTCAAGATTAGCCCCCGTTATGTTGTCAGGTACATACCTGCAACGTGCGGGGGTTTTCTC

Structures

Toxin

• AlphaFold DB: A0A4P7TSJ7

Antitoxin