Detailed information of TA system TA140420

Bioinformatically predicted

Overview

TA module

• Type: I
• Classification (family/domain): ldrD-rdlD/Ldr(toxin)
• Location: 3954256..3954478
• Replicon: chromosome
• Accession: NZ_CP044158
• Organism: Shigella flexneri strain AR-0423

Toxin (Protein)

• Gene name: ldrD
• Uniprot ID: S1NWX0
• Locus tag: F4V35_RS20470
• Protein ID: WP_001295224.1
• Coordinates: 3954256..3954363 (-)
• Length: 36 a.a.

Antitoxin (RNA)

Gene name	rdlD
Locus tag	-
Coordinates	3954412..3954478 (+)

Genomic Context

Locus tag	Coordinates	Strand	Size (bp)	Protein ID	Product	Description
F4V35_RS20425	3949285..3950856	+	1572	WP_001204920.1	cellulose biosynthesis c-di-GMP-binding protein BcsE	-
F4V35_RS20430	3950853..3951044	+	192	WP_000988299.1	cellulose biosynthesis protein BcsF	-
F4V35_RS20435	3951041..3952720	+	1680	WP_000191557.1	cellulose biosynthesis protein BcsG	-
F4V35_RS20440	3952807..3952914	-	108	WP_001295224.1	type I toxin-antitoxin system toxin Ldr family protein	-
-	3952971..3953026	+	56	NuclAT_28	-	-
-	3952971..3953026	+	56	NuclAT_28	-	-
-	3952971..3953026	+	56	NuclAT_28	-	-
-	3952971..3953026	+	56	NuclAT_28	-	-
-	3952971..3953026	+	56	NuclAT_31	-	-
-	3952971..3953026	+	56	NuclAT_31	-	-
-	3952971..3953026	+	56	NuclAT_31	-	-
-	3952971..3953026	+	56	NuclAT_31	-	-
-	3952971..3953026	+	56	NuclAT_34	-	-
-	3952971..3953026	+	56	NuclAT_34	-	-
-	3952971..3953026	+	56	NuclAT_34	-	-
-	3952971..3953026	+	56	NuclAT_34	-	-
-	3952971..3953026	+	56	NuclAT_37	-	-
-	3952971..3953026	+	56	NuclAT_37	-	-
-	3952971..3953026	+	56	NuclAT_37	-	-
-	3952971..3953026	+	56	NuclAT_37	-	-
-	3952971..3953028	+	58	NuclAT_22	-	-
-	3952971..3953028	+	58	NuclAT_22	-	-
-	3952971..3953028	+	58	NuclAT_22	-	-
-	3952971..3953028	+	58	NuclAT_22	-	-
-	3952971..3953028	+	58	NuclAT_25	-	-
-	3952971..3953028	+	58	NuclAT_25	-	-
-	3952971..3953028	+	58	NuclAT_25	-	-
-	3952971..3953028	+	58	NuclAT_25	-	-
F4V35_RS20450	3953290..3953397	-	108	WP_001295224.1	type I toxin-antitoxin system toxin Ldr family protein	-
-	3953454..3953509	+	56	NuclAT_30	-	-
-	3953454..3953509	+	56	NuclAT_30	-	-
-	3953454..3953509	+	56	NuclAT_30	-	-
-	3953454..3953509	+	56	NuclAT_30	-	-
-	3953454..3953509	+	56	NuclAT_33	-	-
-	3953454..3953509	+	56	NuclAT_33	-	-
-	3953454..3953509	+	56	NuclAT_33	-	-
-	3953454..3953509	+	56	NuclAT_33	-	-
-	3953454..3953509	+	56	NuclAT_36	-	-
-	3953454..3953509	+	56	NuclAT_36	-	-
-	3953454..3953509	+	56	NuclAT_36	-	-
-	3953454..3953509	+	56	NuclAT_36	-	-
-	3953454..3953509	+	56	NuclAT_39	-	-
-	3953454..3953509	+	56	NuclAT_39	-	-
-	3953454..3953509	+	56	NuclAT_39	-	-
-	3953454..3953509	+	56	NuclAT_39	-	-
-	3953454..3953511	+	58	NuclAT_24	-	-
-	3953454..3953511	+	58	NuclAT_24	-	-
-	3953454..3953511	+	58	NuclAT_24	-	-
-	3953454..3953511	+	58	NuclAT_24	-	-
-	3953454..3953511	+	58	NuclAT_27	-	-
-	3953454..3953511	+	58	NuclAT_27	-	-
-	3953454..3953511	+	58	NuclAT_27	-	-
-	3953454..3953511	+	58	NuclAT_27	-	-
F4V35_RS20460	3953773..3953880	-	108	WP_000141634.1	type I toxin-antitoxin system toxic polypeptide LdrD	-
-	3953938..3953992	+	55	NuclAT_29	-	-
-	3953938..3953992	+	55	NuclAT_29	-	-
-	3953938..3953992	+	55	NuclAT_29	-	-
-	3953938..3953992	+	55	NuclAT_29	-	-
-	3953938..3953992	+	55	NuclAT_32	-	-
-	3953938..3953992	+	55	NuclAT_32	-	-
-	3953938..3953992	+	55	NuclAT_32	-	-
-	3953938..3953992	+	55	NuclAT_32	-	-
-	3953938..3953992	+	55	NuclAT_35	-	-
-	3953938..3953992	+	55	NuclAT_35	-	-
-	3953938..3953992	+	55	NuclAT_35	-	-
-	3953938..3953992	+	55	NuclAT_35	-	-
-	3953938..3953992	+	55	NuclAT_38	-	-
-	3953938..3953992	+	55	NuclAT_38	-	-
-	3953938..3953992	+	55	NuclAT_38	-	-
-	3953938..3953992	+	55	NuclAT_38	-	-
-	3953938..3953994	+	57	NuclAT_23	-	-
-	3953938..3953994	+	57	NuclAT_23	-	-
-	3953938..3953994	+	57	NuclAT_23	-	-
-	3953938..3953994	+	57	NuclAT_23	-	-
-	3953938..3953994	+	57	NuclAT_26	-	-
-	3953938..3953994	+	57	NuclAT_26	-	-
-	3953938..3953994	+	57	NuclAT_26	-	-
-	3953938..3953994	+	57	NuclAT_26	-	-
F4V35_RS20470	3954256..3954363	-	108	WP_001295224.1	type I toxin-antitoxin system toxin Ldr family protein	Toxin
-	3954412..3954478	+	67	-	-	Antitoxin
F4V35_RS20480	3954839..3956110	+	1272	WP_005052340.1	aromatic amino acid transport family protein	-
F4V35_RS20485	3956140..3957144	-	1005	WP_000107041.1	dipeptide ABC transporter ATP-binding subunit DppF	-
F4V35_RS20490	3957141..3958124	-	984	WP_001196486.1	dipeptide ABC transporter ATP-binding protein	-
F4V35_RS20495	3958135..3959037	-	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

>T140420 WP_001295224.1 NZ_CP044158:c3954363-3954256 [Shigella flexneri]
MTLAELGMAFWHDLAAPVIAGILASMIVNWLNKRK

Nucleotide

• Length: 108 bp

>T140420 NZ_CP059156:c2547712-2547605 [Staphylococcus aureus]
ATGTTCAATTTATTAATTGACATCATGACTTCAGCTTTAAGCGGCTGTCTTGTTGCGTTTTTTGCACATTGGTTACGAAC
GCGCAACAATAAAAAAGGTGACAAATAA

Antitoxin

Nucleotide

• Length: 67 bp

>AT140420 NZ_CP044158:3954412-3954478 [Shigella flexneri]
GTCTAGGTTCAAGATTAGCCCCCGTTATGTTGTCAGGTACATACCTGCAACGTGCGGGGGTTTTCTC

Structures

Toxin

• AlphaFold DB: A0A4P7TSJ7

Antitoxin