Detailed information of TA system TA140361

Bioinformatically predicted

Overview

TA module

• Type: II
• Classification (family/domain): vapBC/VapC-VagC
• Location: 108519..109144
• Replicon: plasmid pAR-0425-2
• Accession: NZ_CP044154
• Organism: Shigella flexneri strain AR-0425

Toxin (Protein)

• Gene name: vapC
• Uniprot ID: Q7BEJ1
• Locus tag: F4V37_RS24190
• Protein ID: WP_000911311.1
• Coordinates: 108746..109144 (+)
• Length: 133 a.a.

Antitoxin (Protein)

• Gene name: vapB
• Uniprot ID: Q7BEJ0
• Locus tag: F4V37_RS24185
• Protein ID: WP_000450531.1
• Coordinates: 108519..108746 (+)
• Length: 76 a.a.

Genomic Context

Locus tag	Coordinates	Strand	Size (bp)	Protein ID	Product	Description
F4V37_RS24185	108519..108746	+	228	WP_000450531.1	toxin-antitoxin system antitoxin VapB	Antitoxin
F4V37_RS24190	108746..109144	+	399	WP_000911311.1	type II toxin-antitoxin system VapC family toxin	Toxin
F4V37_RS24195	109153..109332	-	180	Protein_133	hypothetical protein	-
F4V37_RS24200	109377..110533	+	1157	WP_094081572.1	IS3 family transposase	-
F4V37_RS24205	110578..111501	+	924	Protein_135	IS630 family transposase	-
F4V37_RS24210	111655..112599	-	945	WP_004996485.1	lauroyl-Kdo(2)-lipid IV(A) myristoyltransferase	-
F4V37_RS24215	112664..113614	-	951	WP_015683210.1	virulence factor VirK	-

Associated MGEs

MGE detail	Similar MGEs	Relative position	MGE Type	Cargo ARG	Virulence gene	Coordinates	Length (bp)
	-	inside	Non-Mobilizable plasmid	-	ospC1 / ospD3/senA / ipaH4.5 / ipaH7.8 / ospC2 / ipaH7.8 / ipaH2.5 / ipaH2.5 / ospE1 / ipgB2 / ospD1 / ospF / ospD2 / ospC2 / ospC4 / ospB / ospB / icsP/sopA / nleE / ospE1 / ipaH1.4 / ospG / ipaH9.8 / ospI / papC / icsA/virG / virA / spa40 / spa29 / spa9 / spa24 / spa33 / spa32 / spa13 / spa47 / 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	1..222114	222114

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

>T140361 WP_000911311.1 NZ_CP044154:108746-109144 [Shigella flexneri]
MLKFMLDTNICIFTIKNKPASVRERFNLNQGKMCISSVTLMELIYGAEKSQMPERNLAVIEGFVSRIDVLDYDAAAATHT
GQIRAELARQGRPVGPFDQMIAGHARSRGLIIVTNNTREFERVGGLRTEDWS

Nucleotide

• Length: 399 bp

>T140361 NZ_CP059125:4037652-4038116 [Escherichia coli]
ATGGATTTTCCACAAAGGGTTAATGGTTGGGCGCTATATGCTCATCCCTGTTTTCAGGAAACCTACGATGCTTTAGTTGC
CGAAGTCGAGGCATTAAAGGGAAAAGATCCTGAAAATTATCAGAGAAAAGCTGCCACAAAGTTATTGGCGGTGGTCCATA
AAGTGATTGAGGAGCATATCACGGTCAATCCATCATCACCGGCATTCCGTCATGGCAAGTCGTTAGGCTCTGGGAAAAAT
AAAGACTGGTCACGGGTAAAATTTGGTGCTGGTCGCTATCGTCTCTTCTTTCGTTACAGTGAAAAAGAGAAAGTCATCAT
TCTGGGATGGATGAACGATGAAAACACGCTGCGCACCTACGGTAAAAAAACAGATGCCTATACCGTATTCAGTAAAATGT
TAAAAAGAGGACATCCTCCTGCCGACTGGGAAAGCCTCACCCAAGAGACAGAAGAAAACCATTGA

Antitoxin

Protein

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

>AT140361 WP_000450531.1 NZ_CP044154:108519-108746 [Shigella flexneri]
METTVFLSNRSQAVRLPKAVALPENVKRVEVIAVGRTRIITPAGETWDEWFDGHSVSTDFMDNREQPGMQERESF

Nucleotide

• Length: 228 bp

>AT140361 NZ_CP059125:4037317-4037652 [Escherichia coli]
ATGCCCGCTAATGCTCGCTCTCACGCTGTACTGACCACTGAATCAAAGGTCACGATACGCGGACAAACAACTATCCCCGC
GCCAGTGCGTGAGGCCTTAAAACTGAAGCCAGGCCAGGACAGCATTCATTACGAAATTCTGCCTGGTGGGCAAGTCTTTA
TGTGCCGACTGGGAGATGAACAGGAGGATCATACTATGAATGCATTTTTGCGTTTTCTGGATGCAGATATCCAGAACAAC
CCGCAAAAAACTCGTCCATTCAACATTCAACAAGGAAAGAAACTTGTCGCTGGCATGGACGTCAACATTGATGATGAGAT
TGGCGACGACGAATAA

Structures

Toxin

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

Antitoxin

• PDB: 3TND
• AlphaFold DB: Q7BEJ0