Detailed information of TA system TA143813

Bioinformatically predicted

Overview

TA module

• Type: II
• Classification (family/domain): vapBC/VapC-VagC
• Location: 16880..17505
• Replicon: plasmid unnamed1
• Accession: NZ_CP046285
• Organism: Shigella sonnei strain FDAARGOS_715

Toxin (Protein)

• Gene name: vapC
• Uniprot ID: Q6XVU6
• Locus tag: FOC23_RS00090
• Protein ID: WP_000911318.1
• Coordinates: 16880..17278 (-)
• Length: 133 a.a.

Antitoxin (Protein)

• Gene name: vapB
• Uniprot ID: Q31SG2
• Locus tag: FOC23_RS00095
• Protein ID: WP_000450530.1
• Coordinates: 17278..17505 (-)
• Length: 76 a.a.

Genomic Context

Locus tag	Coordinates	Strand	Size (bp)	Protein ID	Product	Description
FOC23_RS25555	12946..13284	+	339	Protein_11	antirestriction protein	-
FOC23_RS00075 (FOC23_00075)	13350..14506	+	1157	WP_087879933.1	IS3-like element IS600 family transposase	-
FOC23_RS00080 (FOC23_00080)	14549..14680	+	132	Protein_13	IS1 family transposase	-
FOC23_RS00085 (FOC23_00085)	14706..16871	+	2166	WP_000492721.1	type IV conjugative transfer system coupling protein TraD	-
FOC23_RS00090 (FOC23_00090)	16880..17278	-	399	WP_000911318.1	type II toxin-antitoxin system VapC family toxin	Toxin
FOC23_RS00095 (FOC23_00095)	17278..17505	-	228	WP_000450530.1	toxin-antitoxin system antitoxin VapB	Antitoxin
FOC23_RS00100 (FOC23_00100)	17587..19803	+	2217	Protein_17	conjugative transfer relaxase/helicase TraI	-

Associated MGEs

MGE detail	Similar MGEs	Relative position	MGE Type	Cargo ARG	Virulence gene	Coordinates	Length (bp)
	-	inside	Non-Mobilizable plasmid	-	ipaH1.4 / tviC / nleE / icsP/sopA / ospB / ospC3 / ospD2 / ospF / ospD1 / ipgB2 / ospE2 / ospC1 / ospD3/senA / ipaH7.8 / ipaH4.5 / ospC2 / ospC3 / ipaJ / ipaA / ipaD / ipaC / ipaB / ipgC / ipgB1 / ipgA / icsB / ipgD / ipgE / ipgF / mxiG / mxiH / mxiI / mxiJ / mxiK / mxiN / mxiL / mxiM / mxiE / mxiD / mxiC / mxiA / spa15 / spa47 / spa13 / spa32 / spa33 / spa24 / spa9 / spa29 / spa40 / virA / icsA/virG / papC / ospI / ipaH9.8 / ospG	1..213386	213386
	-	inside	IScluster/Tn	-	ipaH1.4	19847..40862	21015

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: 14845.09 Da
• Isoelectric Point: 8.5264

>T143813 WP_000911318.1 NZ_CP046285:c17278-16880 [Shigella sonnei]
MLKFMLDTNICIFTIKNKPASVRERFNLNQGRMCISSVTLMELIYGAEKSQMPERNLAVIEGFVSRIDVLDYDAAAATHT
GQIRAELARQGRPVGPFDQMIAGHARSRGLIIVTNNTREFERVGGLRTEDWS

Nucleotide

• Length: 399 bp

>T143813 NZ_CP061371:c3124-2702 [Komagataeibacter rhaeticus]
ATGATCCTGCTCGATACAAATGTGATCTCGGAGCCGTGGAAGCCCGTCCCGGAGCAGCGTGTTCTGGCCTGGATCGATGG
ACAGGCGATCGAGACGCTTTTTCTGTCTGCCGTCACGGTGGCGGAACTGCGTTTCGGGATCGGGGCGATGCCGTCTGGTC
GGCGGCGTTCTGTACTGCATGAGCGGCTGGAACAGGAGGTATTGCCCTTGTTCGCGGGGCGTGTCCTGTCGTTCGATCTG
GCGGCGTCCCAGGCCTATGCCGAACTGATGGTGCGGGCCAGGTCAGAAGGTCGGGCGATTGGCAAGGCAGATGGCTATAT
TGCAGCAACCGCTGCATCCCGGGGTTATGTCGTGGCCAGCCGCGACGTGTCTCCTTTCGAGGCGGCTGGTGTGCGGGTTC
TCAATCCGTGGGAGGATACCTGA

Antitoxin

Protein

• Length: 76 a.a.
• Molecular weight: 8535.59 Da
• Isoelectric Point: 4.7513

>AT143813 WP_000450530.1 NZ_CP046285:c17505-17278 [Shigella sonnei]
METTVFLSNRSQAVRLPKAVALPENVKRVEVIAVGRTRIITPAGETWDEWFDGHSVSADFMDNREQPGMQERESF

Nucleotide

• Length: 228 bp

>AT143813 NZ_CP061371:c3372-3121 [Komagataeibacter rhaeticus]
ATGTCTTCTGTGGTTATTCGTAATCTTCCGGAAGAGACGCATCGGGCGCTGAAGGCGCAGGCCATGCTGCATGGACGCAG
TACGGAAGCGGAGATCCGGACCATTCTGGAAGCGGCCGTCCGGCCGCCGCAGCGGGTCCGGCTGGGATCGCTTCTGGCGT
CCATCGGTCGGGAGGCCGGTGTGTGTGATCAGGATATTGCGGCCTTGCAGAGCCGCGATCAGACCCCGGCCGAGCCGATG
TCCTTCGAATGA

Structures

Toxin

• PDB: 6SD6

Antitoxin

• AlphaFold DB: Q31SG2