Detailed information of TA system TA024929

Bioinformatically predicted

Overview

TA module

• Type: II
• Classification (family/domain): vagCD/VapC-VagC
• Location: 2159524..2160167
• Replicon: chromosome
• Accession: NC_014562
• Organism: Pantoea vagans C9-1

Toxin (Protein)

• Gene name: vagD
• Uniprot ID: E1SJ90
• Locus tag: PVAG_RS14045
• Protein ID: WP_013358527.1
• Coordinates: 2159751..2160167 (+)
• Length: 139 a.a.

Antitoxin (Protein)

• Gene name: vagC
• Uniprot ID: E1SJ89
• Locus tag: PVAG_RS14040
• Protein ID: WP_013358526.1
• Coordinates: 2159524..2159754 (+)
• Length: 77 a.a.

Genomic Context

Locus tag	Coordinates	Strand	Size (bp)	Protein ID	Product	Description
PVAG_RS14025	2155219..2156931	-	1713	WP_013358522.1	PTS fructose transporter subunit IIBC	-
PVAG_RS14030	2156948..2157886	-	939	WP_013358523.1	1-phosphofructokinase	-
PVAG_RS14035	2157883..2159013	-	1131	WP_013358524.1	fused PTS fructose transporter subunit IIA/HPr protein	-
PVAG_RS14040	2159524..2159754	+	231	WP_013358526.1	AbrB/MazE/SpoVT family DNA-binding domain-containing protein	Antitoxin
PVAG_RS14045	2159751..2160167	+	417	WP_013358527.1	type II toxin-antitoxin system VapC family toxin	Toxin
PVAG_RS23090	2160204..2160458	-	255	WP_071822187.1	YkgJ family cysteine cluster protein	-
PVAG_RS14050	2160790..2161362	+	573	WP_003854146.1	elongation factor P-like protein YeiP	-
PVAG_RS14055	2161437..2162405	+	969	WP_013358528.1	GTP-binding protein	-
PVAG_RS14060	2162449..2163156	+	708	WP_013358529.1	phosphatase PAP2 family protein	-
PVAG_RS14065	2163670..2164245	+	576	WP_013358530.1	bifunctional murein DD-endopeptidase/murein LD-carboxypeptidase	-

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 (7-51)

Sequences

Toxin

Protein

• Length: 139 a.a.
• Molecular weight: 15340.68 Da
• Isoelectric Point: 7.9128

>T24929 WP_013358527.1 NC_014562:2159751-2160167 [Pantoea vagans C9-1]
VNNTYMLDTNICSFIMREQPEEVIRRLEQAVLRNHRIVVSAITYAEMRFGTIGKKASPRHMHLVDAFCARLDAVLSWDRA
AIDTTTEIKAALAAVGTPIGPNDTAIAGHAIAARAILVTNNTREFQRVPGLQLEDWVK

Nucleotide

• Length: 417 bp

>T24929 NC_014562:2159751-2160167 [Pantoea vagans C9-1]
GTGAACAACACTTACATGCTCGACACAAATATCTGCTCATTTATTATGCGTGAGCAGCCTGAAGAAGTCATCCGGCGACT
GGAACAGGCGGTGCTGCGTAACCACCGGATTGTGGTTTCTGCAATTACTTATGCTGAAATGCGTTTCGGTACGATCGGAA
AGAAAGCTTCACCGCGGCATATGCATTTGGTCGATGCATTCTGCGCACGGCTTGATGCTGTACTGTCATGGGACCGTGCA
GCGATAGATACAACCACTGAAATCAAAGCAGCGCTGGCTGCTGTCGGAACGCCCATTGGTCCTAACGACACTGCGATTGC
CGGGCATGCTATTGCGGCCAGGGCTATTCTGGTGACCAATAACACACGCGAGTTTCAACGGGTACCCGGATTGCAGCTGG
AAGACTGGGTCAAATAA

Antitoxin

Protein

• Length: 77 a.a.
• Molecular weight: 8889.01 Da
• Isoelectric Point: 4.4992

>AT24929 WP_013358526.1 NC_014562:2159524-2159754 [Pantoea vagans C9-1]
MRTVSVFKNGNNRAIRLPRDMDFEGVSELEIIREGDAIILRPVRPTWRSFTQLEKADSDFMTEREDVISDEGRFDL

Nucleotide

• Length: 231 bp

>AT24929 NC_014562:2159524-2159754 [Pantoea vagans C9-1]
ATGAGAACCGTCTCTGTATTCAAAAATGGCAATAATCGCGCCATTCGCCTGCCTCGCGACATGGATTTTGAGGGAGTGAG
CGAGCTGGAAATTATCAGGGAAGGAGATGCTATTATTCTGCGTCCTGTCAGACCCACATGGCGTTCATTTACCCAGCTTG
AGAAAGCTGACTCTGACTTCATGACAGAGCGTGAAGACGTTATCAGCGATGAGGGACGTTTTGACCTGTGA

Structures

Toxin

• AlphaFold DB: E1SJ90

Antitoxin

• AlphaFold DB: E1SJ89