Detailed information of TA system TA021338

Bioinformatically predicted

Overview

TA module

• Type: II
• Classification (family/domain): vapBC/VapC-VagC
• Location: 102220..102845
• Replicon: plasmid pSB4_227
• Accession: NC_007608
• Organism: Shigella boydii Sb227

Toxin (Protein)

• Gene name: vapC
• Uniprot ID: Q6XVU6
• Locus tag: SBO_RS25485
• Protein ID: WP_000911318.1
• Coordinates: 102220..102618 (-)
• Length: 133 a.a.

Antitoxin (Protein)

• Gene name: vapB
• Uniprot ID: Q31SG2
• Locus tag: SBO_RS25490
• Protein ID: WP_000450530.1
• Coordinates: 102618..102845 (-)
• Length: 76 a.a.

Genomic Context

Locus tag	Coordinates	Strand	Size (bp)	Protein ID	Product	Description
SBO_RS25455	98185..99135	+	951	WP_005059240.1	virulence factor VirK	-
SBO_RS25460	99200..100144	+	945	WP_005027201.1	lauroyl-Kdo(2)-lipid IV(A) myristoyltransferase	-
SBO_RS25465	100298..100969	-	672	Protein_122	IS630 family transposase	-
SBO_RS25470	100985..101682	-	698	Protein_123	IS1 family transposase	-
SBO_RS25480	101738..102211	+	474	Protein_124	conjugal transfer protein TraD	-
SBO_RS25485	102220..102618	-	399	WP_000911318.1	tRNA(fMet)-specific endonuclease VapC	Toxin
SBO_RS25490	102618..102845	-	228	WP_000450530.1	toxin-antitoxin system antitoxin VapB	Antitoxin
SBO_RS29015	102927..103346	+	420	WP_011379081.1	conjugative relaxase	-

Associated MGEs

MGE detail	Similar MGEs	Relative position	MGE Type	Cargo ARG	Virulence gene	Coordinates	Length (bp)
	-	inside	Non-Mobilizable plasmid	-	ospB / ospC4 / ospC4 / ospD2 / ospF / ospD1 / ipgB2 / ipaH1.4 / ipaH4.5 / ipaH7.8 / ospD3/senA / ospC1 / senB / ospE2 / ospI / ospC3 / ipaH9.8 / ospC2 / nleE / icsP/sopA	1..126697	126697
	-	inside	IScluster/Tn	-	ospE2 / ospI / ospC3 / ipaH9.8	70356..101488	31132

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

>T21338 WP_000911318.1 NC_007608:c102618-102220 [Shigella boydii Sb227]
MLKFMLDTNICIFTIKNKPASVRERFNLNQGRMCISSVTLMELIYGAEKSQMPERNLAVIEGFVSRIDVLDYDAAAATHT
GQIRAELARQGRPVGPFDQMIAGHARSRGLIIVTNNTREFERVGGLRTEDWS

Nucleotide

• Length: 399 bp

>T21338 NC_007608:c102618-102220 [Shigella boydii Sb227]
ATGCTGAAGTTTATGCTCGATACCAACATCTGCATTTTTACGATAAAGAACAAACCCGCCAGCGTCAGGGAGCGTTTTAA
CCTGAACCAGGGGAGAATGTGTATCAGTTCGGTCACCCTGATGGAGCTGATATATGGTGCAGAAAAAAGCCAGATGCCTG
AACGTAATCTCGCTGTGATCGAGGGATTTGTTTCCCGCATTGATGTTCTGGATTACGACGCTGCTGCAGCCACACACACC
GGCCAGATAAGAGCAGAACTTGCCCGTCAGGGACGCCCTGTCGGGCCATTTGATCAAATGATCGCAGGTCATGCCCGCAG
TCGGGGGCTGATTATTGTGACTAATAACACCCGGGAATTTGAACGTGTGGGCGGCCTGAGAACTGAAGACTGGAGCTGA

Antitoxin

Protein

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

>AT21338 WP_000450530.1 NC_007608:c102845-102618 [Shigella boydii Sb227]
METTVFLSNRSQAVRLPKAVALPENVKRVEVIAVGRTRIITPAGETWDEWFDGHSVSADFMDNREQPGMQERESF

Nucleotide

• Length: 228 bp

>AT21338 NC_007608:c102845-102618 [Shigella boydii Sb227]
ATGGAAACCACCGTATTTCTCAGCAACCGCAGCCAGGCGGTCAGACTGCCAAAAGCGGTTGCATTGCCGGAAAACGTAAA
ACGCGTTGAAGTGATTGCTGTCGGACGAACCAGAATCATTACGCCAGCCGGAGAGACATGGGACGAATGGTTCGACGGAC
ACAGCGTCAGCGCCGATTTTATGGATAACAGGGAACAGCCCGGCATGCAGGAAAGGGAGTCATTCTGA

Structures

Toxin

• PDB: 6SD6

Antitoxin

• AlphaFold DB: Q31SG2