Detailed information of TA system TA170329

Bioinformatically predicted

Overview

TA module

• Type: II
• Classification (family/domain): vagCD/VapC-VagC
• Location: 3087115..3087764
• Replicon: chromosome
• Accession: NZ_CP060401
• Organism: Xenorhabdus nematophila strain SII

Toxin (Protein)

• Gene name: vagD
• Uniprot ID: D3VI06
• Locus tag: H8F46_RS13500
• Protein ID: WP_013183266.1
• Coordinates: 3087115..3087540 (-)
• Length: 142 a.a.

Antitoxin (Protein)

• Gene name: vagC
• Uniprot ID: N1NH79
• Locus tag: H8F46_RS13505
• Protein ID: WP_010845293.1
• Coordinates: 3087537..3087764 (-)
• Length: 76 a.a.

Genomic Context

Locus tag	Coordinates	Strand	Size (bp)	Protein ID	Product	Description
H8F46_RS13475	3082235..3084061	-	1827	WP_038218872.1	ATP-dependent DNA helicase RecQ	-
H8F46_RS13480	3084190..3084927	-	738	Protein_2633	phospholipase A	-
H8F46_RS13485	3085110..3085595	+	486	WP_010845290.1	thioesterase family protein	-
H8F46_RS13490	3085644..3085802	+	159	WP_113935524.1	hypothetical protein	-
H8F46_RS13495	3086090..3086980	+	891	WP_010845291.1	EamA family transporter RarD	-
H8F46_RS13500	3087115..3087540	-	426	WP_013183266.1	type II toxin-antitoxin system VapC family toxin	Toxin
H8F46_RS13505	3087537..3087764	-	228	WP_010845293.1	AbrB/MazE/SpoVT family DNA-binding domain-containing protein	Antitoxin
H8F46_RS13510	3088027..3088977	-	951	WP_010845294.1	magnesium/cobalt transporter CorA	-
H8F46_RS13515	3089066..3091240	-	2175	WP_065814196.1	DNA helicase II	-
H8F46_RS13520	3091287..3092003	-	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

>T170329 WP_013183266.1 NZ_CP060401:c3087540-3087115 [Xenorhabdus nematophila]
MKTVYMLDTNICSFIMREQPVAVIKQLQRCVMNNHLIVVSAITYAEMRFGAVGKKASPKHIVLVDEFCRRLDKILPWDKS
AVDATTKTKIALAAAGTPIGHNDAAIAGHALSVGATLITNNSREFSRVTGLSLEDWANGLI

Nucleotide

• Length: 426 bp

>T170329 NZ_CP077290:c2620343-2619945 [Enterobacter cancerogenus]
ATGAGGCATATGCTGGATACGAATATTGTGAGTCATCTGTTTAAAAGGCACCCAGGCGTAATAAACAGAATGGCTTGCCT
GACACCGGACGACGTTTGCATATCCAGTATTACAGAAGCAGAGCTGCTCTACGGTGCCGATAAAAAACAAAGCGAGAGGC
TGAAAAAAACAATCCAGGCGTTTCTGAGCACCATCACCGTCTGCGACTGGGACAGCGAGGCCGCAGCCACCTACGGCGCG
CTCCGTGCAGCGATGGAAAAGAGAGGCAACGTCATGGGCGATCTCGACCAGCTGATCGCTGCGCATGCCATCAGCCAGGG
CACCACCATTGTCACGAACGATCGTGCTTTTCTGATGGTGCAGGAGTTAAGCGTGGAAGACTGGACGCACGCTGCCTGA

Antitoxin

Protein

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

>AT170329 WP_010845293.1 NZ_CP060401:c3087764-3087537 [Xenorhabdus nematophila]
MRTVAIFKNGNNRAIRLPKDLDFEGVNELEIIREGEAIILRPIKPSWDSFLYEDKADADFLSERPDIVEEGRVNL

Nucleotide

• Length: 228 bp

>AT170329 NZ_CP077290:c2620606-2620340 [Enterobacter cancerogenus]
ATGGAACGCAAAGCAAAACTGTTTAAAAGAGGGCGAAGCCAGGCGGTAATGCTGCCTGCTGAATTCACCTTTGATGCGGA
GAGTGTTTATATCCGGCGGGATGACGACGGGAATGTGGTGCTGTCGGAGAAGTCCGCCAGCACCAGGAGCTGGGATAATT
TTTTCAGACTGCTGGAAAACACATCTGTACCTGAAAACTTTTTGAGTAAGGAGGAGAGAAACCAGAGCATAACCAGAAGA
GACCCGCTGGATGGAGTTCAGGGATGA

Structures

Toxin

• AlphaFold DB: D3VI06

Antitoxin

• AlphaFold DB: N1NH79