Detailed information of TA system TA120381

Bioinformatically predicted

Overview

TA module

• Type: II
• Classification (family/domain): vapBC/VapC-VagC
• Location: 112700..113325
• Replicon: plasmid pWR100
• Accession: NZ_CP037924
• Organism: Shigella flexneri 5a str. M90T

Toxin (Protein)

• Gene name: vapC
• Uniprot ID: Q7BEJ1
• Locus tag: EKN05_RS24205
• Protein ID: WP_000911311.1
• Coordinates: 112927..113325 (+)
• Length: 133 a.a.

Antitoxin (Protein)

• Gene name: vapB
• Uniprot ID: Q7BEJ0
• Locus tag: EKN05_RS24200
• Protein ID: WP_000450531.1
• Coordinates: 112700..112927 (+)
• Length: 76 a.a.

Genomic Context

Locus tag	Coordinates	Strand	Size (bp)	Protein ID	Product	Description
EKN05_RS24200 (EKN05_024220)	112700..112927	+	228	WP_000450531.1	toxin-antitoxin system antitoxin VapB	Antitoxin
EKN05_RS24205 (EKN05_024225)	112927..113325	+	399	WP_000911311.1	type II toxin-antitoxin system VapC family toxin	Toxin
EKN05_RS24210 (EKN05_024230)	113334..113513	-	180	Protein_138	hypothetical protein	-
EKN05_RS24215 (EKN05_024235)	113558..114714	+	1157	WP_094106057.1	IS3-like element IS600 family transposase	-
EKN05_RS24220 (EKN05_024240)	114759..115682	+	924	Protein_140	IS630-like element IS630 family transposase	-
EKN05_RS24225 (EKN05_024245)	115836..116780	-	945	WP_004996485.1	lauroyl-Kdo(2)-lipid IV(A) myristoyltransferase	-
EKN05_RS24230 (EKN05_024250)	116845..117795	-	951	WP_004970430.1	virulence factor VirK	-

Associated MGEs

MGE detail	Similar MGEs	Relative position	MGE Type	Cargo ARG	Virulence gene	Coordinates	Length (bp)
	-	inside	Non-Mobilizable plasmid	-	ospC2 / ospC1 / ospD3/senA / ipaH4.5 / ipaH7.8 / ospC2 / ipaH2.5 / ospE2 / ipgB2 / ospD1 / ospF / ospD2 / ospC2 / ospC4 / ospC4 / ospB / icsP/sopA / nleE / ospE1 / ipaH1.4 / ospG / ipaH9.8 / ospI / papC / icsA/virG / virA / spa40 / spa29 / spa9 / spa24 / spa33 / spa32 / spa13 / spa47 / spa15 / mxiA / mxiC / mxiD / mxiE / mxiM / mxiL / mxiN / mxiK / mxiJ / mxiI / mxiH / mxiG / ipgF / ipgE / ipgD / icsB / ipgA / ipgB1 / ipgC / ipaB / ipaC / ipaD / ipaA / ipaJ / ospC3 / ospC1 / ospD3/senA	1..232195	232195

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

• PIN domain (5-125)

Antitoxin

• SpoVT-AbrB domain (7-51)

Sequences

Toxin

Protein

• Length: 133 a.a.
• Molecular weight: 14817.08 Da
• Isoelectric Point: 8.5232

>T120381 WP_000911311.1 NZ_CP037924:112927-113325 [Shigella flexneri 5a str. M90T]
MLKFMLDTNICIFTIKNKPASVRERFNLNQGKMCISSVTLMELIYGAEKSQMPERNLAVIEGFVSRIDVLDYDAAAATHT
GQIRAELARQGRPVGPFDQMIAGHARSRGLIIVTNNTREFERVGGLRTEDWS

Nucleotide

• Length: 399 bp

>T120381 NZ_CP037924:112927-113325 [Shigella flexneri 5a str. M90T]
ATGCTGAAGTTTATGCTCGATACCAACATCTGCATTTTTACGATAAAGAACAAACCCGCCAGCGTCAGGGAGCGTTTTAA
CCTGAACCAGGGGAAAATGTGTATCAGTTCGGTCACCCTGATGGAGCTGATATATGGTGCAGAAAAAAGCCAGATGCCTG
AACGTAATCTCGCTGTGATCGAGGGATTTGTTTCCCGCATTGATGTTCTGGATTACGACGCTGCTGCAGCCACACACACC
GGCCAGATAAGAGCAGAACTTGCCCGTCAGGGACGCCCTGTCGGGCCATTTGATCAAATGATCGCAGGTCATGCCCGCAG
TCGGGGGCTGATTATTGTGACTAATAACACCCGGGAATTTGAACGTGTGGGCGGCCTGAGAACTGAAGACTGGAGCTGA

Antitoxin

Protein

• Length: 76 a.a.
• Molecular weight: 8565.62 Da
• Isoelectric Point: 4.7513

>AT120381 WP_000450531.1 NZ_CP037924:112700-112927 [Shigella flexneri 5a str. M90T]
METTVFLSNRSQAVRLPKAVALPENVKRVEVIAVGRTRIITPAGETWDEWFDGHSVSTDFMDNREQPGMQERESF

Nucleotide

• Length: 228 bp

>AT120381 NZ_CP037924:112700-112927 [Shigella flexneri 5a str. M90T]
ATGGAAACCACCGTATTTCTCAGCAACCGCAGCCAGGCGGTCAGACTGCCAAAAGCGGTTGCATTGCCGGAAAACGTAAA
ACGCGTTGAAGTGATTGCTGTCGGACGAACCAGAATCATTACGCCAGCCGGAGAGACATGGGACGAATGGTTCGACGGAC
ACAGCGTCAGCACCGATTTTATGGATAACAGGGAACAGCCCGGCATGCAGGAAAGGGAGTCATTCTGA

Structures

Toxin

• PDB: 3TND
• PDB: 5ED0
• PDB: 5ECW
• PDB: 5ECD
• PDB: 5ECY

Antitoxin

• PDB: 3TND
• AlphaFold DB: Q7BEJ0