Detailed information of TA system TA087711

Bioinformatically predicted

Overview

TA module

• Type: I
• Classification (family/domain): ldrD-rdlD/Ldr(toxin)
• Location: 1056888..1057110
• Replicon: chromosome
• Accession: NZ_CP024473
• Organism: Shigella flexneri 7b strain 94-3007

Toxin (Protein)

• Gene name: ldrD
• Uniprot ID: S1NWX0
• Locus tag: CPZ98_RS05345
• Protein ID: WP_001295224.1
• Coordinates: 1056888..1056995 (-)
• Length: 36 a.a.

Antitoxin (RNA)

Gene name	rdlD
Locus tag	-
Coordinates	1057044..1057110 (+)

Genomic Context

Locus tag	Coordinates	Strand	Size (bp)	Protein ID	Product	Description
CPZ98_RS05300	1051917..1053488	+	1572	WP_001204920.1	cellulose biosynthesis c-di-GMP-binding protein BcsE	-
CPZ98_RS05305	1053485..1053676	+	192	WP_000988299.1	cellulose biosynthesis protein BcsF	-
CPZ98_RS05310	1053673..1055352	+	1680	WP_000191557.1	cellulose biosynthesis protein BcsG	-
CPZ98_RS05315	1055439..1055546	-	108	WP_001295224.1	type I toxin-antitoxin system toxin Ldr family protein	-
-	1055603..1055658	+	56	NuclAT_28	-	-
-	1055603..1055658	+	56	NuclAT_28	-	-
-	1055603..1055658	+	56	NuclAT_28	-	-
-	1055603..1055658	+	56	NuclAT_28	-	-
-	1055603..1055658	+	56	NuclAT_31	-	-
-	1055603..1055658	+	56	NuclAT_31	-	-
-	1055603..1055658	+	56	NuclAT_31	-	-
-	1055603..1055658	+	56	NuclAT_31	-	-
-	1055603..1055658	+	56	NuclAT_34	-	-
-	1055603..1055658	+	56	NuclAT_34	-	-
-	1055603..1055658	+	56	NuclAT_34	-	-
-	1055603..1055658	+	56	NuclAT_34	-	-
-	1055603..1055658	+	56	NuclAT_37	-	-
-	1055603..1055658	+	56	NuclAT_37	-	-
-	1055603..1055658	+	56	NuclAT_37	-	-
-	1055603..1055658	+	56	NuclAT_37	-	-
-	1055603..1055660	+	58	NuclAT_22	-	-
-	1055603..1055660	+	58	NuclAT_22	-	-
-	1055603..1055660	+	58	NuclAT_22	-	-
-	1055603..1055660	+	58	NuclAT_22	-	-
-	1055603..1055660	+	58	NuclAT_25	-	-
-	1055603..1055660	+	58	NuclAT_25	-	-
-	1055603..1055660	+	58	NuclAT_25	-	-
-	1055603..1055660	+	58	NuclAT_25	-	-
CPZ98_RS05325	1055922..1056029	-	108	WP_001295224.1	type I toxin-antitoxin system toxin Ldr family protein	-
-	1056086..1056141	+	56	NuclAT_30	-	-
-	1056086..1056141	+	56	NuclAT_30	-	-
-	1056086..1056141	+	56	NuclAT_30	-	-
-	1056086..1056141	+	56	NuclAT_30	-	-
-	1056086..1056141	+	56	NuclAT_33	-	-
-	1056086..1056141	+	56	NuclAT_33	-	-
-	1056086..1056141	+	56	NuclAT_33	-	-
-	1056086..1056141	+	56	NuclAT_33	-	-
-	1056086..1056141	+	56	NuclAT_36	-	-
-	1056086..1056141	+	56	NuclAT_36	-	-
-	1056086..1056141	+	56	NuclAT_36	-	-
-	1056086..1056141	+	56	NuclAT_36	-	-
-	1056086..1056141	+	56	NuclAT_39	-	-
-	1056086..1056141	+	56	NuclAT_39	-	-
-	1056086..1056141	+	56	NuclAT_39	-	-
-	1056086..1056141	+	56	NuclAT_39	-	-
-	1056086..1056143	+	58	NuclAT_24	-	-
-	1056086..1056143	+	58	NuclAT_24	-	-
-	1056086..1056143	+	58	NuclAT_24	-	-
-	1056086..1056143	+	58	NuclAT_24	-	-
-	1056086..1056143	+	58	NuclAT_27	-	-
-	1056086..1056143	+	58	NuclAT_27	-	-
-	1056086..1056143	+	58	NuclAT_27	-	-
-	1056086..1056143	+	58	NuclAT_27	-	-
CPZ98_RS05335	1056405..1056512	-	108	WP_000141634.1	type I toxin-antitoxin system toxic polypeptide LdrD	-
-	1056570..1056624	+	55	NuclAT_29	-	-
-	1056570..1056624	+	55	NuclAT_29	-	-
-	1056570..1056624	+	55	NuclAT_29	-	-
-	1056570..1056624	+	55	NuclAT_29	-	-
-	1056570..1056624	+	55	NuclAT_32	-	-
-	1056570..1056624	+	55	NuclAT_32	-	-
-	1056570..1056624	+	55	NuclAT_32	-	-
-	1056570..1056624	+	55	NuclAT_32	-	-
-	1056570..1056624	+	55	NuclAT_35	-	-
-	1056570..1056624	+	55	NuclAT_35	-	-
-	1056570..1056624	+	55	NuclAT_35	-	-
-	1056570..1056624	+	55	NuclAT_35	-	-
-	1056570..1056624	+	55	NuclAT_38	-	-
-	1056570..1056624	+	55	NuclAT_38	-	-
-	1056570..1056624	+	55	NuclAT_38	-	-
-	1056570..1056624	+	55	NuclAT_38	-	-
-	1056570..1056626	+	57	NuclAT_23	-	-
-	1056570..1056626	+	57	NuclAT_23	-	-
-	1056570..1056626	+	57	NuclAT_23	-	-
-	1056570..1056626	+	57	NuclAT_23	-	-
-	1056570..1056626	+	57	NuclAT_26	-	-
-	1056570..1056626	+	57	NuclAT_26	-	-
-	1056570..1056626	+	57	NuclAT_26	-	-
-	1056570..1056626	+	57	NuclAT_26	-	-
CPZ98_RS05345	1056888..1056995	-	108	WP_001295224.1	type I toxin-antitoxin system toxin Ldr family protein	Toxin
-	1057044..1057110	+	67	-	-	Antitoxin
CPZ98_RS05350	1057471..1058742	+	1272	WP_005052340.1	aromatic amino acid transport family protein	-
CPZ98_RS05355	1058772..1059776	-	1005	WP_000107041.1	dipeptide ABC transporter ATP-binding subunit DppF	-
CPZ98_RS05360	1059773..1060756	-	984	WP_001196486.1	dipeptide ABC transporter ATP-binding protein	-
CPZ98_RS05365	1060767..1061669	-	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

>T87711 WP_001295224.1 NZ_CP024473:c1056995-1056888 [Shigella flexneri 7b]
MTLAELGMAFWHDLAAPVIAGILASMIVNWLNKRK

Nucleotide

• Length: 108 bp

>T87711 NZ_CP024473:c1056995-1056888 [Shigella flexneri 7b]
ATGACGCTCGCAGAGCTGGGCATGGCCTTCTGGCATGATTTAGCGGCTCCGGTCATTGCTGGCATTCTTGCCAGTATGAT
CGTGAACTGGCTGAACAAGCGGAAGTAG

Antitoxin

Nucleotide

• Length: 67 bp

>AT87711 NZ_CP024473:1057044-1057110 [Shigella flexneri 7b]
GTCTAGGTTCAAGATTAGCCCCCGTTATGTTGTCAGGTACATACCTGCAACGTGCGGGGGTTTTCTC

Structures

Toxin

• AlphaFold DB: A0A4P7TSJ7

Antitoxin