Detailed information of TA system TA021648

Bioinformatically predicted

Overview

TA module

• Type: I
• Classification (family/domain): ldrD-rdlD/Ldr(toxin)
• Location: 1278771..1278982
• Replicon: chromosome
• Accession: NC_008258
• Organism: Shigella flexneri 5 str. 8401

Toxin (Protein)

• Gene name: ldrD
• Uniprot ID: S1PGT3
• Locus tag: SFV_RS06845
• Protein ID: WP_000170954.1
• Coordinates: 1278771..1278878 (-)
• Length: 36 a.a.

Antitoxin (RNA)

Gene name	rdlD
Locus tag	-
Coordinates	1278928..1278982 (+)

Genomic Context

Locus tag	Coordinates	Strand	Size (bp)	Protein ID	Product	Description
SFV_RS06820	1274615..1275697	+	1083	WP_000804726.1	peptide chain release factor 1	-
SFV_RS06825	1275697..1276530	+	834	WP_000456468.1	peptide chain release factor N(5)-glutamine methyltransferase	-
SFV_RS06830	1276527..1276919	+	393	WP_000200378.1	invasion regulator SirB2	-
SFV_RS06835	1276923..1277732	+	810	WP_001257041.1	invasion regulator SirB1	-
SFV_RS06840	1277768..1278622	+	855	WP_000811065.1	3-deoxy-8-phosphooctulonate synthase	-
SFV_RS06845	1278771..1278878	-	108	WP_000170954.1	type I toxin-antitoxin system toxin Ldr family protein	Toxin
-	1278928..1278982	+	55	NuclAT_18	-	Antitoxin
-	1278928..1278982	+	55	NuclAT_18	-	Antitoxin
-	1278928..1278982	+	55	NuclAT_18	-	Antitoxin
-	1278928..1278982	+	55	NuclAT_18	-	Antitoxin
-	1278928..1278982	+	55	NuclAT_20	-	Antitoxin
-	1278928..1278982	+	55	NuclAT_20	-	Antitoxin
-	1278928..1278982	+	55	NuclAT_20	-	Antitoxin
-	1278928..1278982	+	55	NuclAT_20	-	Antitoxin
-	1278928..1278982	+	55	NuclAT_22	-	Antitoxin
-	1278928..1278982	+	55	NuclAT_22	-	Antitoxin
-	1278928..1278982	+	55	NuclAT_22	-	Antitoxin
-	1278928..1278982	+	55	NuclAT_22	-	Antitoxin
-	1278928..1278982	+	55	NuclAT_24	-	Antitoxin
-	1278928..1278982	+	55	NuclAT_24	-	Antitoxin
-	1278928..1278982	+	55	NuclAT_24	-	Antitoxin
-	1278928..1278982	+	55	NuclAT_24	-	Antitoxin
-	1278928..1278982	+	55	NuclAT_26	-	Antitoxin
-	1278928..1278982	+	55	NuclAT_26	-	Antitoxin
-	1278928..1278982	+	55	NuclAT_26	-	Antitoxin
-	1278928..1278982	+	55	NuclAT_26	-	Antitoxin
-	1278928..1278982	+	55	NuclAT_28	-	Antitoxin
-	1278928..1278982	+	55	NuclAT_28	-	Antitoxin
-	1278928..1278982	+	55	NuclAT_28	-	Antitoxin
-	1278928..1278982	+	55	NuclAT_28	-	Antitoxin
SFV_RS06850	1278996..1280342	-	1347	WP_011069251.1	IS4 family transposase	-
SFV_RS06855	1280744..1280851	-	108	WP_000170961.1	type I toxin-antitoxin system toxin Ldr family protein	-
-	1280899..1280964	+	66	NuclAT_17	-	-
-	1280899..1280964	+	66	NuclAT_17	-	-
-	1280899..1280964	+	66	NuclAT_17	-	-
-	1280899..1280964	+	66	NuclAT_17	-	-
-	1280899..1280964	+	66	NuclAT_19	-	-
-	1280899..1280964	+	66	NuclAT_19	-	-
-	1280899..1280964	+	66	NuclAT_19	-	-
-	1280899..1280964	+	66	NuclAT_19	-	-
-	1280899..1280964	+	66	NuclAT_21	-	-
-	1280899..1280964	+	66	NuclAT_21	-	-
-	1280899..1280964	+	66	NuclAT_21	-	-
-	1280899..1280964	+	66	NuclAT_21	-	-
-	1280899..1280964	+	66	NuclAT_23	-	-
-	1280899..1280964	+	66	NuclAT_23	-	-
-	1280899..1280964	+	66	NuclAT_23	-	-
-	1280899..1280964	+	66	NuclAT_23	-	-
-	1280899..1280964	+	66	NuclAT_25	-	-
-	1280899..1280964	+	66	NuclAT_25	-	-
-	1280899..1280964	+	66	NuclAT_25	-	-
-	1280899..1280964	+	66	NuclAT_25	-	-
-	1280899..1280964	+	66	NuclAT_27	-	-
-	1280899..1280964	+	66	NuclAT_27	-	-
-	1280899..1280964	+	66	NuclAT_27	-	-
-	1280899..1280964	+	66	NuclAT_27	-	-
-	1280899..1280966	+	68	NuclAT_11	-	-
-	1280899..1280966	+	68	NuclAT_11	-	-
-	1280899..1280966	+	68	NuclAT_11	-	-
-	1280899..1280966	+	68	NuclAT_11	-	-
-	1280899..1280966	+	68	NuclAT_12	-	-
-	1280899..1280966	+	68	NuclAT_12	-	-
-	1280899..1280966	+	68	NuclAT_12	-	-
-	1280899..1280966	+	68	NuclAT_12	-	-
-	1280899..1280966	+	68	NuclAT_13	-	-
-	1280899..1280966	+	68	NuclAT_13	-	-
-	1280899..1280966	+	68	NuclAT_13	-	-
-	1280899..1280966	+	68	NuclAT_13	-	-
-	1280899..1280966	+	68	NuclAT_14	-	-
-	1280899..1280966	+	68	NuclAT_14	-	-
-	1280899..1280966	+	68	NuclAT_14	-	-
-	1280899..1280966	+	68	NuclAT_14	-	-
-	1280899..1280966	+	68	NuclAT_15	-	-
-	1280899..1280966	+	68	NuclAT_15	-	-
-	1280899..1280966	+	68	NuclAT_15	-	-
-	1280899..1280966	+	68	NuclAT_15	-	-
-	1280899..1280966	+	68	NuclAT_16	-	-
-	1280899..1280966	+	68	NuclAT_16	-	-
-	1280899..1280966	+	68	NuclAT_16	-	-
-	1280899..1280966	+	68	NuclAT_16	-	-
SFV_RS06860	1281256..1282356	-	1101	WP_000063614.1	sodium-potassium/proton antiporter ChaA	-
SFV_RS06865	1282626..1282856	+	231	WP_001146444.1	putative cation transport regulator ChaB	-
SFV_RS06870	1283014..1283709	+	696	WP_001295621.1	glutathione-specific gamma-glutamylcyclotransferase	-

Associated MGEs

MGE detail	Similar MGEs	Relative position	MGE Type	Cargo ARG	Virulence gene	Coordinates	Length (bp)
	Similar MGE(s) Similar MGE(s) is defined as other TA-related MGE(s) with Mash distance < 0.01 to this MGE. Detail Genome accession Organism MGE type Related TA Coordinates Mash distance View NZ_CP037923 Shigella flexneri 5a str. M90T 1937675..1939003 0.002	flank	IS/Tn	-	-	1278996..1280324	1328

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: 3983.80 Da
• Isoelectric Point: 11.4779

>T21648 WP_000170954.1 NC_008258:c1278878-1278771 [Shigella flexneri 5 str. 8401]
MTLAQFAMIFWHDLAAPILAGIITAAIVGWWRNRK

Nucleotide

• Length: 108 bp

>T21648 NC_008258:c1278878-1278771 [Shigella flexneri 5 str. 8401]
ATGACGCTCGCGCAGTTTGCCATGATTTTCTGGCACGACCTGGCAGCACCGATCCTGGCGGGAATTATTACCGCAGCGAT
TGTCGGCTGGTGGCGTAACCGGAAGTAA

Antitoxin

Nucleotide

• Length: 55 bp

>AT21648 NC_008258:1278928-1278982 [Shigella flexneri 5 str. 8401]
TCTGGTTCAAGATTAGCCCCCGTTCTGTTGTCAGGTTAAACCTCTCAACGTGCGG

Structures

Toxin

• AlphaFold DB: A0A7U9LPE9

Antitoxin