Detailed information of TA system TA111657

Bioinformatically predicted

Overview

TA module

• Type: II
• Classification (family/domain): vagCD/VapC-VagC
• Location: 3087066..3087715
• Replicon: chromosome
• Accession: NZ_CP032329
• Organism: Xenorhabdus nematophila strain YL001

Toxin (Protein)

• Gene name: vagD
• Uniprot ID: D3VI06
• Locus tag: D3790_RS13770
• Protein ID: WP_013183266.1
• Coordinates: 3087066..3087491 (-)
• Length: 142 a.a.

Antitoxin (Protein)

• Gene name: vagC
• Uniprot ID: N1NH79
• Locus tag: D3790_RS13775
• Protein ID: WP_010845293.1
• Coordinates: 3087488..3087715 (-)
• Length: 76 a.a.

Genomic Context

Locus tag	Coordinates	Strand	Size (bp)	Protein ID	Product	Description
D3790_RS13745	3082186..3084012	-	1827	WP_038218872.1	ATP-dependent DNA helicase RecQ	-
D3790_RS13750	3084141..3084878	-	738	Protein_2637	phospholipase A	-
D3790_RS13755	3085061..3085546	+	486	WP_010845290.1	thioesterase family protein	-
D3790_RS13760	3085595..3085753	+	159	WP_113935524.1	hypothetical protein	-
D3790_RS13765	3086041..3086931	+	891	WP_010845291.1	EamA family transporter RarD	-
D3790_RS13770	3087066..3087491	-	426	WP_013183266.1	type II toxin-antitoxin system VapC family toxin	Toxin
D3790_RS13775	3087488..3087715	-	228	WP_010845293.1	AbrB/MazE/SpoVT family DNA-binding domain-containing protein	Antitoxin
D3790_RS13780	3087978..3088928	-	951	WP_010845294.1	magnesium/cobalt transporter CorA	-
D3790_RS13785	3089017..3091191	-	2175	WP_065814196.1	DNA helicase II	-
D3790_RS13790	3091238..3091954	-	717	WP_010845296.1	5-amino-6-(5-phospho-D-ribitylamino)uracil phosphatase YigB	-

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 (5-129)

Antitoxin

• SpoVT-AbrB domain (7-50)

Sequences

Toxin

Protein

• Length: 142 a.a.
• Molecular weight: 15366.95 Da
• Isoelectric Point: 9.2397

>T111657 WP_013183266.1 NZ_CP032329:c3087491-3087066 [Xenorhabdus nematophila]
MKTVYMLDTNICSFIMREQPVAVIKQLQRCVMNNHLIVVSAITYAEMRFGAVGKKASPKHIVLVDEFCRRLDKILPWDKS
AVDATTKTKIALAAAGTPIGHNDAAIAGHALSVGATLITNNSREFSRVTGLSLEDWANGLI

Nucleotide

• Length: 426 bp

>T111657 NZ_CP032329:c3087491-3087066 [Xenorhabdus nematophila]
ATGAAAACGGTTTACATGCTGGATACCAATATTTGTTCATTCATTATGCGTGAACAACCTGTTGCAGTAATTAAACAATT
ACAGAGATGCGTGATGAATAACCATCTGATCGTTGTATCTGCGATTACTTATGCGGAAATGCGCTTCGGGGCAGTCGGAA
AGAAAGCTTCCCCGAAACATATTGTATTAGTTGATGAGTTTTGTAGACGATTAGATAAAATTTTACCTTGGGATAAATCC
GCGGTAGACGCAACAACTAAAACAAAGATTGCATTAGCTGCTGCTGGAACGCCTATTGGACATAATGATGCTGCTATTGC
AGGGCATGCTTTGTCTGTAGGAGCGACATTGATAACAAACAATAGTCGTGAATTTTCTCGTGTCACTGGACTATCATTAG
AAGATTGGGCTAACGGGCTGATTTAA

Antitoxin

Protein

• Length: 76 a.a.
• Molecular weight: 8659.82 Da
• Isoelectric Point: 4.3775

>AT111657 WP_010845293.1 NZ_CP032329:c3087715-3087488 [Xenorhabdus nematophila]
MRTVAIFKNGNNRAIRLPKDLDFEGVNELEIIREGEAIILRPIKPSWDSFLYEDKADADFLSERPDIVEEGRVNL

Nucleotide

• Length: 228 bp

>AT111657 NZ_CP032329:c3087715-3087488 [Xenorhabdus nematophila]
ATGCGAACTGTAGCGATTTTTAAAAATGGTAATAATCGCGCTATCCGTTTACCTAAAGATCTGGATTTTGAAGGCGTAAA
TGAACTGGAGATTATCCGTGAAGGAGAAGCCATTATATTGCGTCCGATAAAACCCAGTTGGGATTCATTTCTTTATGAGG
ACAAAGCAGACGCAGATTTTCTGTCTGAACGCCCAGATATTGTCGAGGAAGGGCGTGTGAATTTATGA

Structures

Toxin

• AlphaFold DB: D3VI06

Antitoxin

• AlphaFold DB: N1NH79