Detailed information of TA system TA115068

Bioinformatically predicted

Overview

TA module

• Type: II
• Classification (family/domain): vapBC/VapC-VagC
• Location: 58076..58701
• Replicon: plasmid unnamed1
• Accession: NZ_CP034059
• Organism: Shigella flexneri strain FDAARGOS_535

Toxin (Protein)

• Gene name: vapC
• Uniprot ID: -
• Locus tag: EGX88_RS00440
• Protein ID: WP_000911087.1
• Coordinates: 58303..58701 (+)
• Length: 133 a.a.

Antitoxin (Protein)

• Gene name: vapB
• Uniprot ID: Q7BEJ0
• Locus tag: EGX88_RS00435
• Protein ID: WP_000450531.1
• Coordinates: 58076..58303 (+)
• Length: 76 a.a.

Genomic Context

Locus tag	Coordinates	Strand	Size (bp)	Protein ID	Product	Description
EGX88_RS00435 (EGX88_00430)	58076..58303	+	228	WP_000450531.1	toxin-antitoxin system antitoxin VapB	Antitoxin
EGX88_RS00440 (EGX88_00435)	58303..58701	+	399	WP_000911087.1	tRNA(fMet)-specific endonuclease VapC	Toxin
EGX88_RS00445 (EGX88_00440)	58710..58889	-	180	Protein_78	hypothetical protein	-
EGX88_RS00450 (EGX88_00445)	58934..60090	+	1157	WP_134797086.1	IS3 family transposase	-
EGX88_RS00455 (EGX88_00450)	60101..60987	+	887	Protein_80	IS630 family transposase	-
EGX88_RS00460 (EGX88_00455)	61141..62085	-	945	WP_004996485.1	lauroyl-Kdo(2)-lipid IV(A) myristoyltransferase	-
EGX88_RS00465 (EGX88_00460)	62150..63100	-	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 / ipgB2 / ospD1 / ospF / ospD2 / 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 / ipaH4.5 / ipaH7.8 / ospE2 / ipaH2.5	1..217451	217451

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: 14799.04 Da
• Isoelectric Point: 8.5232

>T115068 WP_000911087.1 NZ_CP034059:58303-58701 [Shigella flexneri]
MLKFILDTNICIFTIKNKPASVRERFNLNQGKMCISSVTLMELIYGAEKSQMPERNLAVIEGFVSRIDVLDYDAAAATHT
GQIRAELARQGRPVGPFDQMIAGHARSRGLIIVTNNTREFERVGGLRTEDWS

Nucleotide

• Length: 399 bp

>T115068 NZ_CP034059:58303-58701 [Shigella flexneri]
ATGCTGAAGTTTATTCTCGATACCAACATCTGCATTTTTACGATAAAGAACAAACCCGCCAGCGTCAGGGAGCGTTTTAA
CCTGAACCAGGGGAAAATGTGTATCAGTTCGGTCACCCTGATGGAGCTGATATATGGTGCAGAAAAAAGCCAGATGCCTG
AACGTAATCTCGCTGTGATCGAGGGATTTGTTTCCCGCATTGATGTTCTGGATTACGACGCTGCTGCAGCCACACACACC
GGCCAGATAAGAGCAGAACTTGCCCGTCAGGGACGCCCTGTCGGGCCATTTGATCAAATGATCGCAGGTCATGCCCGCAG
TCGGGGGCTGATTATTGTGACTAATAACACCCGGGAATTTGAACGTGTGGGCGGCCTGAGAACTGAAGACTGGAGCTGA

Antitoxin

Protein

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

>AT115068 WP_000450531.1 NZ_CP034059:58076-58303 [Shigella flexneri]
METTVFLSNRSQAVRLPKAVALPENVKRVEVIAVGRTRIITPAGETWDEWFDGHSVSTDFMDNREQPGMQERESF

Nucleotide

• Length: 228 bp

>AT115068 NZ_CP034059:58076-58303 [Shigella flexneri]
ATGGAAACCACCGTATTTCTCAGCAACCGCAGCCAGGCGGTCAGACTGCCAAAAGCGGTTGCATTGCCGGAAAACGTAAA
ACGCGTTGAAGTGATTGCTGTCGGACGAACCAGAATCATTACGCCAGCCGGAGAGACATGGGACGAATGGTTCGACGGAC
ACAGCGTCAGCACCGATTTTATGGATAACAGGGAACAGCCCGGCATGCAGGAAAGGGAGTCATTCTGA

Structures

Antitoxin

• AlphaFold DB: Q7BEJ0