Detailed information of TA system TA120606

Bioinformatically predicted

Overview

TA module

• Type: I
• Classification (family/domain): ldrD-rdlD/Ldr(toxin)
• Location: 378715..378937
• Replicon: chromosome
• Accession: NZ_CP037996
• Organism: Shigella flexneri strain FC906

Toxin (Protein)

• Gene name: ldrD
• Uniprot ID: S1NWX0
• Locus tag: CBL25_RS01975
• Protein ID: WP_001295224.1
• Coordinates: 378715..378822 (-)
• Length: 36 a.a.

Antitoxin (RNA)

Gene name	rdlD
Locus tag	-
Coordinates	378871..378937 (+)

Genomic Context

Locus tag	Coordinates	Strand	Size (bp)	Protein ID	Product	Description
CBL25_RS01930	373744..375315	+	1572	WP_001204920.1	cellulose biosynthesis c-di-GMP-binding protein BcsE	-
CBL25_RS01935	375312..375503	+	192	WP_000988299.1	cellulose biosynthesis protein BcsF	-
CBL25_RS01940	375500..377179	+	1680	WP_000191557.1	cellulose biosynthesis protein BcsG	-
CBL25_RS01945	377266..377373	-	108	WP_001295224.1	type I toxin-antitoxin system toxin Ldr family protein	-
-	377430..377485	+	56	NuclAT_28	-	-
-	377430..377485	+	56	NuclAT_28	-	-
-	377430..377485	+	56	NuclAT_28	-	-
-	377430..377485	+	56	NuclAT_28	-	-
-	377430..377485	+	56	NuclAT_31	-	-
-	377430..377485	+	56	NuclAT_31	-	-
-	377430..377485	+	56	NuclAT_31	-	-
-	377430..377485	+	56	NuclAT_31	-	-
-	377430..377485	+	56	NuclAT_34	-	-
-	377430..377485	+	56	NuclAT_34	-	-
-	377430..377485	+	56	NuclAT_34	-	-
-	377430..377485	+	56	NuclAT_34	-	-
-	377430..377485	+	56	NuclAT_37	-	-
-	377430..377485	+	56	NuclAT_37	-	-
-	377430..377485	+	56	NuclAT_37	-	-
-	377430..377485	+	56	NuclAT_37	-	-
-	377430..377487	+	58	NuclAT_22	-	-
-	377430..377487	+	58	NuclAT_22	-	-
-	377430..377487	+	58	NuclAT_22	-	-
-	377430..377487	+	58	NuclAT_22	-	-
-	377430..377487	+	58	NuclAT_25	-	-
-	377430..377487	+	58	NuclAT_25	-	-
-	377430..377487	+	58	NuclAT_25	-	-
-	377430..377487	+	58	NuclAT_25	-	-
CBL25_RS01955	377749..377856	-	108	WP_001295224.1	type I toxin-antitoxin system toxin Ldr family protein	-
-	377913..377968	+	56	NuclAT_30	-	-
-	377913..377968	+	56	NuclAT_30	-	-
-	377913..377968	+	56	NuclAT_30	-	-
-	377913..377968	+	56	NuclAT_30	-	-
-	377913..377968	+	56	NuclAT_33	-	-
-	377913..377968	+	56	NuclAT_33	-	-
-	377913..377968	+	56	NuclAT_33	-	-
-	377913..377968	+	56	NuclAT_33	-	-
-	377913..377968	+	56	NuclAT_36	-	-
-	377913..377968	+	56	NuclAT_36	-	-
-	377913..377968	+	56	NuclAT_36	-	-
-	377913..377968	+	56	NuclAT_36	-	-
-	377913..377968	+	56	NuclAT_39	-	-
-	377913..377968	+	56	NuclAT_39	-	-
-	377913..377968	+	56	NuclAT_39	-	-
-	377913..377968	+	56	NuclAT_39	-	-
-	377913..377970	+	58	NuclAT_24	-	-
-	377913..377970	+	58	NuclAT_24	-	-
-	377913..377970	+	58	NuclAT_24	-	-
-	377913..377970	+	58	NuclAT_24	-	-
-	377913..377970	+	58	NuclAT_27	-	-
-	377913..377970	+	58	NuclAT_27	-	-
-	377913..377970	+	58	NuclAT_27	-	-
-	377913..377970	+	58	NuclAT_27	-	-
CBL25_RS01965	378232..378339	-	108	WP_000141634.1	type I toxin-antitoxin system toxic polypeptide LdrD	-
-	378397..378451	+	55	NuclAT_29	-	-
-	378397..378451	+	55	NuclAT_29	-	-
-	378397..378451	+	55	NuclAT_29	-	-
-	378397..378451	+	55	NuclAT_29	-	-
-	378397..378451	+	55	NuclAT_32	-	-
-	378397..378451	+	55	NuclAT_32	-	-
-	378397..378451	+	55	NuclAT_32	-	-
-	378397..378451	+	55	NuclAT_32	-	-
-	378397..378451	+	55	NuclAT_35	-	-
-	378397..378451	+	55	NuclAT_35	-	-
-	378397..378451	+	55	NuclAT_35	-	-
-	378397..378451	+	55	NuclAT_35	-	-
-	378397..378451	+	55	NuclAT_38	-	-
-	378397..378451	+	55	NuclAT_38	-	-
-	378397..378451	+	55	NuclAT_38	-	-
-	378397..378451	+	55	NuclAT_38	-	-
-	378397..378453	+	57	NuclAT_23	-	-
-	378397..378453	+	57	NuclAT_23	-	-
-	378397..378453	+	57	NuclAT_23	-	-
-	378397..378453	+	57	NuclAT_23	-	-
-	378397..378453	+	57	NuclAT_26	-	-
-	378397..378453	+	57	NuclAT_26	-	-
-	378397..378453	+	57	NuclAT_26	-	-
-	378397..378453	+	57	NuclAT_26	-	-
CBL25_RS01975	378715..378822	-	108	WP_001295224.1	type I toxin-antitoxin system toxin Ldr family protein	Toxin
-	378871..378937	+	67	-	-	Antitoxin
CBL25_RS01980	379298..380569	+	1272	WP_005052340.1	aromatic amino acid transport family protein	-
CBL25_RS01985	380599..381603	-	1005	WP_000107041.1	dipeptide ABC transporter ATP-binding subunit DppF	-
CBL25_RS01990	381600..382583	-	984	WP_001196486.1	dipeptide ABC transporter ATP-binding protein	-
CBL25_RS01995	382594..383496	-	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

>T120606 WP_001295224.1 NZ_CP037996:c378822-378715 [Shigella flexneri]
MTLAELGMAFWHDLAAPVIAGILASMIVNWLNKRK

Nucleotide

• Length: 108 bp

>T120606 NZ_CP037996:c378822-378715 [Shigella flexneri]
ATGACGCTCGCAGAGCTGGGCATGGCCTTCTGGCATGATTTAGCGGCTCCGGTCATTGCTGGCATTCTTGCCAGTATGAT
CGTGAACTGGCTGAACAAGCGGAAGTAG

Antitoxin

Nucleotide

• Length: 67 bp

>AT120606 NZ_CP037996:378871-378937 [Shigella flexneri]
GTCTAGGTTCAAGATTAGCCCCCGTTATGTTGTCAGGTACATACCTGCAACGTGCGGGGGTTTTCTC

Structures

Toxin

• AlphaFold DB: A0A4P7TSJ7

Antitoxin