Detailed information of TA system TA084628

Bioinformatically predicted

Overview

TA module

• Type: II
• Classification (family/domain): vapBC/PIN(toxin)
• Location: 2869527..2870164
• Replicon: chromosome
• Accession: NZ_CP023621
• Organism: Mycobacterium tuberculosis strain LN2900

Toxin (Protein)

• Gene name: vapC
• Uniprot ID: P0DMV7
• Locus tag: CP477_RS13965
• Protein ID: WP_003413180.1
• Coordinates: 2869527..2869922 (-)
• Length: 132 a.a.

Antitoxin (Protein)

• Gene name: vapB
• Uniprot ID: P9WJ44
• Locus tag: CP477_RS13970
• Protein ID: WP_003413183.1
• Coordinates: 2869919..2870164 (-)
• Length: 82 a.a.

Genomic Context

Locus tag	Coordinates	Strand	Size (bp)	Protein ID	Product	Description
CP477_RS13920	2864930..2866141	+	1212	WP_003900845.1	alpha/beta hydrolase family protein	-
CP477_RS13930	2866268..2866927	+	660	WP_003900846.1	LppA family lipoprotein	-
CP477_RS13935	2866924..2867586	+	663	WP_003900848.1	hypothetical protein	-
CP477_RS13940	2867583..2867861	+	279	WP_003901422.1	type II toxin-antitoxin system VapB family antitoxin	-
CP477_RS13945	2867954..2868367	+	414	WP_003413164.1	PIN domain nuclease	-
CP477_RS13950	2868406..2868663	+	258	WP_003413167.1	ribbon-helix-helix domain-containing protein	-
CP477_RS13955	2868660..2869037	+	378	WP_003413174.1	type II toxin-antitoxin system VapC family toxin	-
CP477_RS13960	2869053..2869427	-	375	WP_003413177.1	hypothetical protein	-
CP477_RS13965	2869527..2869922	-	396	WP_003413180.1	type II toxin-antitoxin system toxin 23S rRNA-specific endonuclease VapC20	Toxin
CP477_RS13970	2869919..2870164	-	246	WP_003413183.1	type II toxin-antitoxin system antitoxin VapB20	Antitoxin
CP477_RS13980	2870575..2870994	-	420	WP_003413190.1	A24 family peptidase	-
CP477_RS13985	2871006..2871815	-	810	WP_003413193.1	shikimate dehydrogenase	-
CP477_RS13990	2871812..2873065	-	1254	WP_003413196.1	endolytic transglycosylase MltG	-
CP477_RS13995	2873058..2873570	-	513	WP_003413197.1	Holliday junction resolvase RuvX	-

Associated MGEs

MGE detail	Similar MGEs	Relative position	MGE Type	Cargo ARG	Virulence gene	Coordinates	Length (bp)

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

• Endonuclease VapC20-like (1-129)

Antitoxin

• Ribbon-helix-helix protein, CopG (11-49)

Sequences

Toxin

Protein

• Length: 132 a.a.
• Molecular weight: 14619.53 Da
• Isoelectric Point: 6.9794

>T84628 WP_003413180.1 NZ_CP023621:c2869922-2869527 [Mycobacterium tuberculosis]
MIFVDTSFWAALGNAGDARHGTAKRLWASKPPVVMTSNHVLGETWTLLNRRCGHRAAVAAAAIRLSTVVRVEHVTADLEE
QAWEWLVRHDEREYSFVDATSFAVMRKKGIQNAYAFDGDFSAAGFVEVRPE

Nucleotide

• Length: 396 bp

>T84628 NZ_CP023621:c2869922-2869527 [Mycobacterium tuberculosis]
ATGATCTTCGTCGACACGTCCTTCTGGGCTGCACTTGGCAACGCCGGCGACGCTCGGCACGGCACCGCGAAGAGGTTGTG
GGCCAGCAAACCGCCCGTGGTGATGACCTCCAACCATGTCCTGGGCGAGACCTGGACGCTGCTCAACCGGCGCTGCGGTC
ACCGCGCGGCGGTTGCCGCCGCTGCAATCCGCTTGAGCACCGTCGTTCGCGTCGAGCACGTAACAGCCGACCTGGAAGAG
CAGGCATGGGAATGGCTTGTACGCCACGACGAGCGAGAGTACTCGTTCGTCGATGCCACGAGCTTCGCGGTGATGCGAAA
GAAAGGCATCCAAAATGCGTATGCCTTCGATGGTGACTTCAGCGCGGCCGGATTTGTCGAGGTAAGACCCGAGTAG

Antitoxin

Protein

• Length: 82 a.a.
• Molecular weight: 9098.33 Da
• Isoelectric Point: 5.6007

>AT84628 WP_003413183.1 NZ_CP023621:c2870164-2869919 [Mycobacterium tuberculosis]
MLVAYICHVKRLQIYIDEDVDRALAVEARRRRTSKAALIREYVAEHLRQPGPDPVDAFVGSFVGEADLSASVDDVVYGKH
E

Nucleotide

• Length: 246 bp

>AT84628 NZ_CP023621:c2870164-2869919 [Mycobacterium tuberculosis]
ATGCTAGTGGCGTATATTTGCCATGTGAAAAGGCTGCAGATCTACATCGACGAAGACGTTGACCGAGCGCTTGCTGTTGA
AGCGCGACGGCGGCGGACGTCGAAGGCGGCGCTGATCCGGGAGTACGTCGCTGAGCACCTCCGGCAGCCGGGCCCAGATC
CGGTCGATGCCTTCGTCGGATCGTTCGTGGGGGAAGCCGACTTGTCCGCGTCCGTCGACGACGTGGTTTACGGAAAGCAC
GAATGA

Structures

Toxin

• PDB: 5WZ4
• PDB: 5WZF

Antitoxin

• AlphaFold DB: A0A7U4BW31