Detailed information of TA system TA024808

Bioinformatically predicted

Overview

TA module

• Type: II
• Classification (family/domain): vapBC/VapC-VagC
• Location: 4423408..4424060
• Replicon: chromosome
• Accession: NC_014228
• Organism: Xenorhabdus nematophila ATCC 19061

Toxin (Protein)

• Gene name: vapC
• Uniprot ID: D3VFY8
• Locus tag: XNC1_RS19520
• Protein ID: WP_013185764.1
• Coordinates: 4423408..4423797 (-)
• Length: 130 a.a.

Antitoxin (Protein)

• Gene name: vapB
• Uniprot ID: N1NR17
• Locus tag: XNC1_RS19525
• Protein ID: WP_010846167.1
• Coordinates: 4423797..4424060 (-)
• Length: 88 a.a.

Genomic Context

Locus tag	Coordinates	Strand	Size (bp)	Protein ID	Product	Description
XNC1_RS19495 (XNC1_4626)	4418480..4419694	+	1215	WP_013185760.1	3-oxoadipyl-CoA thiolase	-
XNC1_RS19500 (XNC1_4627)	4419780..4421123	+	1344	WP_013185761.1	phenylacetate--CoA ligase	-
XNC1_RS19505 (XNC1_4629)	4421261..4421539	+	279	WP_010846171.1	DUF1778 domain-containing protein	-
XNC1_RS19510 (XNC1_4630)	4421536..4422036	+	501	WP_013185762.1	GNAT family N-acetyltransferase	-
XNC1_RS19515 (XNC1_4631)	4422124..4423065	+	942	WP_013185763.1	phenylacetic acid degradation operon negative regulatory protein PaaX	-
XNC1_RS19520 (XNC1_4632)	4423408..4423797	-	390	WP_013185764.1	type II toxin-antitoxin system VapC family toxin	Toxin
XNC1_RS19525 (XNC1_4633)	4423797..4424060	-	264	WP_010846167.1	AbrB/MazE/SpoVT family DNA-binding domain-containing protein	Antitoxin
XNC1_RS19530 (XNC1_4635)	4424475..4425515	+	1041	WP_013141539.1	IS481 family transposase	-
XNC1_RS22515	4425799..4426376	-	578	Protein_3881	ISAs1 family transposase	-
XNC1_RS19545 (XNC1_4639)	4426436..4426945	+	510	Protein_3882	IS6 family transposase	-
XNC1_RS19550 (XNC1_4640)	4427133..4428005	-	873	WP_013185768.1	IS630 family transposase	-

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

• PIN domain (2-117)

Antitoxin

No domain identified.

Sequences

Toxin

Protein

• Length: 130 a.a.
• Molecular weight: 14464.48 Da
• Isoelectric Point: 5.1131

>T24808 WP_013185764.1 NC_014228:c4423797-4423408 [Xenorhabdus nematophila ATCC 19061]
MYMLDTNTVSYIFRQNQAVTAKLRTIPPSEICISSITEAELRFGLAKRQNHALEQVVNTFIDSITVYDWDQNAAKTYGTL
RAGMEQTGRTMGTMDQLIAAHALSRELTLVTSDSAFEMVIGLNIENWAK

Nucleotide

• Length: 390 bp

>T24808 NC_014228:c4423797-4423408 [Xenorhabdus nematophila ATCC 19061]
ATGTATATGTTGGATACAAACACGGTCAGCTATATTTTCCGTCAAAATCAGGCGGTAACTGCTAAATTGCGAACCATACC
ACCATCAGAGATATGTATTTCCAGTATCACTGAAGCCGAGTTGCGTTTTGGTTTGGCTAAACGTCAAAATCACGCATTAG
AACAAGTCGTAAATACATTTATTGATTCAATCACTGTTTACGACTGGGATCAAAACGCTGCCAAAACCTATGGGACATTG
CGAGCCGGCATGGAACAGACTGGCCGAACTATGGGGACAATGGATCAACTGATTGCAGCACATGCACTGAGCCGAGAATT
AACTCTCGTTACCAGCGATTCTGCGTTTGAAATGGTTATTGGATTAAATATCGAAAATTGGGCGAAATAG

Antitoxin

Protein

• Length: 88 a.a.
• Molecular weight: 10130.15 Da
• Isoelectric Point: 4.3286

>AT24808 WP_010846167.1 NC_014228:c4424060-4423797 [Xenorhabdus nematophila ATCC 19061]
MERIAKIFKNGRNQAVRLPVAFEFDTDQVYIRKNENGDVILSKNRPSTDNWDNFFNMLSAVSVPDNFLDANDRNQDDTER
DPFEGVF

Nucleotide

• Length: 264 bp

>AT24808 NC_014228:c4424060-4423797 [Xenorhabdus nematophila ATCC 19061]
ATGGAACGAATTGCAAAAATCTTCAAAAACGGACGCAATCAGGCTGTCAGGCTGCCTGTTGCGTTTGAATTTGATACTGA
CCAGGTTTATATCCGAAAAAATGAGAACGGAGACGTTATTCTCTCCAAAAACAGACCGTCTACTGACAATTGGGATAATT
TTTTCAATATGCTCAGTGCGGTATCTGTTCCTGATAATTTTCTGGATGCAAATGATCGTAACCAGGATGACACAGAACGT
GACCCATTCGAGGGCGTTTTCTGA

Structures

Toxin

• AlphaFold DB: D3VFY8

Antitoxin

• AlphaFold DB: N1NR17