Detailed information of TA system TA030056

Bioinformatically predicted

Overview

TA module

• Type: II
• Classification (family/domain): vapBC/PIN(toxin)
• Location: 2864989..2865626
• Replicon: chromosome
• Accession: NC_022350
• Organism: Mycobacterium tuberculosis str. Haarlem

Toxin (Protein)

• Gene name: vapC
• Uniprot ID: P0DMV7
• Locus tag: TBHG_RS13385
• Protein ID: WP_003413180.1
• Coordinates: 2864989..2865384 (-)
• Length: 132 a.a.

Antitoxin (Protein)

• Gene name: vapB
• Uniprot ID: P9WJ44
• Locus tag: TBHG_RS13390
• Protein ID: WP_003413183.1
• Coordinates: 2865381..2865626 (-)
• Length: 82 a.a.

Genomic Context

Locus tag	Coordinates	Strand	Size (bp)	Protein ID	Product	Description
TBHG_RS13345	2861074..2861733	+	660	WP_003900846.1	LppA family lipoprotein	-
TBHG_RS13350	2861730..2862389	+	660	WP_003900847.1	hypothetical protein	-
TBHG_RS13355	2862386..2863048	+	663	WP_003900848.1	hypothetical protein	-
TBHG_RS13360	2863045..2863323	+	279	WP_003901422.1	type II toxin-antitoxin system VapB family antitoxin	-
TBHG_RS13365	2863416..2863829	+	414	WP_003413164.1	PIN domain nuclease	-
TBHG_RS13370	2863868..2864125	+	258	WP_003413167.1	ribbon-helix-helix domain-containing protein	-
TBHG_RS13375	2864122..2864499	+	378	WP_003413174.1	type II toxin-antitoxin system VapC family toxin	-
TBHG_RS13380	2864515..2864889	-	375	WP_003413177.1	hypothetical protein	-
TBHG_RS13385	2864989..2865384	-	396	WP_003413180.1	type II toxin-antitoxin system toxin 23S rRNA-specific endonuclease VapC20	Toxin
TBHG_RS13390	2865381..2865626	-	246	WP_003413183.1	type II toxin-antitoxin system antitoxin VapB20	Antitoxin
TBHG_RS13395	2866037..2866456	-	420	WP_003413190.1	A24 family peptidase	-
TBHG_RS13400	2866468..2867277	-	810	WP_003413193.1	shikimate dehydrogenase	-
TBHG_RS13405	2867274..2868527	-	1254	WP_003413196.1	endolytic transglycosylase MltG	-
TBHG_RS13410	2868520..2869032	-	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

>T30056 WP_003413180.1 NC_022350:c2865384-2864989 [Mycobacterium tuberculosis str. Haarlem]
MIFVDTSFWAALGNAGDARHGTAKRLWASKPPVVMTSNHVLGETWTLLNRRCGHRAAVAAAAIRLSTVVRVEHVTADLEE
QAWEWLVRHDEREYSFVDATSFAVMRKKGIQNAYAFDGDFSAAGFVEVRPE

Nucleotide

• Length: 396 bp

>T30056 NC_022350:c2865384-2864989 [Mycobacterium tuberculosis str. Haarlem]
ATGATCTTCGTCGACACGTCCTTCTGGGCTGCACTTGGCAACGCCGGCGACGCTCGGCACGGCACCGCGAAGAGGTTGTG
GGCCAGCAAACCGCCCGTGGTGATGACCTCCAACCATGTCCTGGGCGAGACCTGGACGCTGCTCAACCGGCGCTGCGGTC
ACCGCGCGGCGGTTGCCGCCGCTGCAATCCGCTTGAGCACCGTCGTTCGCGTCGAGCACGTAACAGCCGACCTGGAAGAG
CAGGCATGGGAATGGCTTGTACGCCACGACGAGCGAGAGTACTCGTTCGTCGATGCCACGAGCTTCGCGGTGATGCGAAA
GAAAGGCATCCAAAATGCGTATGCCTTCGATGGTGACTTCAGCGCGGCCGGATTTGTCGAGGTAAGACCCGAGTAG

Antitoxin

Protein

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

>AT30056 WP_003413183.1 NC_022350:c2865626-2865381 [Mycobacterium tuberculosis str. Haarlem]
MLVAYICHVKRLQIYIDEDVDRALAVEARRRRTSKAALIREYVAEHLRQPGPDPVDAFVGSFVGEADLSASVDDVVYGKH
E

Nucleotide

• Length: 246 bp

>AT30056 NC_022350:c2865626-2865381 [Mycobacterium tuberculosis str. Haarlem]
ATGCTAGTGGCGTATATTTGCCATGTGAAAAGGCTGCAGATCTACATCGACGAAGACGTTGACCGAGCGCTTGCTGTTGA
AGCGCGACGGCGGCGGACGTCGAAGGCGGCGCTGATCCGGGAGTACGTCGCTGAGCACCTCCGGCAGCCGGGCCCAGATC
CGGTCGATGCCTTCGTCGGATCGTTCGTGGGGGAAGCCGACTTGTCCGCGTCCGTCGACGACGTGGTTTACGGAAAGCAC
GAATGA

Structures

Toxin

• PDB: 5WZ4
• PDB: 5WZF

Antitoxin

• AlphaFold DB: A0A7U4BW31