Detailed information of TA system TA020896

Bioinformatically predicted

Overview

TA module

• Type: II
• Classification (family/domain): vapBC/VapC-StbC
• Location: 18458..19131
• Replicon: plasmid pDC3000B
• Accession: NC_004632
• Organism: Pseudomonas syringae pv. tomato str. DC3000

Toxin (Protein)

• Gene name: vapC
• Uniprot ID: Q52562
• Locus tag: PSPTO_RS29170
• Protein ID: WP_005769733.1
• Coordinates: 18458..18877 (-)
• Length: 140 a.a.

Antitoxin (Protein)

• Gene name: vapB
• Uniprot ID: Q48B52
• Locus tag: PSPTO_RS29175
• Protein ID: WP_003381346.1
• Coordinates: 18874..19131 (-)
• Length: 86 a.a.

Genomic Context

Locus tag	Coordinates	Strand	Size (bp)	Protein ID	Product	Description
PSPTO_RS29140	13966..14439	-	474	Protein_12	DUF3757 domain-containing protein	-
PSPTO_RS29145	14664..15407	-	744	WP_044393498.1	class I SAM-dependent methyltransferase	-
PSPTO_RS29150	15706..16129	+	424	Protein_14	IS5 family transposase	-
PSPTO_RS29155	16194..16424	+	231	WP_044393496.1	hypothetical protein	-
PSPTO_RS29160	16446..16799	+	354	WP_011106966.1	hypothetical protein	-
PSPTO_RS29165	17333..18283	+	951	WP_164923181.1	IS5 family transposase	-
PSPTO_RS29170	18458..18877	-	420	WP_005769733.1	type II toxin-antitoxin system VapC family toxin	Toxin
PSPTO_RS29175	18874..19131	-	258	WP_003381346.1	Arc family DNA-binding protein	Antitoxin
PSPTO_RS29180	19504..20451	-	948	WP_005769731.1	hypothetical protein	-
PSPTO_RS29185	20813..21094	-	282	WP_004666803.1	hypothetical protein	-
PSPTO_RS29190	21094..21777	-	684	WP_002556051.1	AAA family ATPase	-
PSPTO_RS29195	22172..22372	+	201	WP_002556050.1	molecular chaperone DnaK	-
PSPTO_RS29200	22410..22631	+	222	WP_005769728.1	hypothetical protein	-
PSPTO_RS29205	22964..23584	-	621	WP_005769724.1	recombinase family protein	-
PSPTO_RS29210	23792..24130	+	339	WP_011106968.1	type II toxin-antitoxin system RelE/ParE family toxin	-

Associated MGEs

MGE detail	Similar MGEs	Relative position	MGE Type	Cargo ARG	Virulence gene	Coordinates	Length (bp)
	-	inside	Non-Mobilizable plasmid	-	-	1..67473	67473
	-	flank	IS/Tn	-	-	17333..18283	950

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 (2-124)

Antitoxin

• Arc-like DNA binding domain (5-46)

Sequences

Toxin

Protein

• Length: 140 a.a.
• Molecular weight: 15138.43 Da
• Isoelectric Point: 4.7010

>T20896 WP_005769733.1 NC_004632:c18877-18458 [Pseudomonas syringae pv. tomato str. DC3000]
MILLDTNVISEPQRREPNAHVLDWIDAQALETLYLSTITVAELRAGIALMPVGKRQDSLRENLEKHLLPMFANRVLSFDM
TCTKAYAELLAKSRAAGLAVETADAFIAAIALANGFTVATRDTGPFEAAGLNVINPWEA

Nucleotide

• Length: 420 bp

>T20896 NC_004632:c18877-18458 [Pseudomonas syringae pv. tomato str. DC3000]
ATGATCCTGCTCGATACGAACGTAATTTCAGAACCGCAGCGCCGAGAGCCCAATGCCCACGTCCTTGACTGGATCGACGC
ACAAGCGCTGGAAACGCTTTATCTGTCCACCATCACGGTAGCCGAGTTGCGTGCTGGTATCGCGCTGATGCCTGTCGGAA
AACGCCAGGATAGCTTGCGTGAAAACCTGGAAAAGCACCTGCTGCCGATGTTCGCCAATAGGGTGCTGTCGTTCGATATG
ACTTGTACGAAGGCTTATGCCGAGCTGCTGGCCAAGTCCCGCGCAGCCGGGTTGGCGGTCGAAACGGCAGATGCCTTCAT
TGCAGCCATCGCCCTCGCCAACGGCTTCACCGTCGCCACCCGTGACACTGGCCCTTTTGAGGCTGCCGGGTTGAACGTCA
TTAACCCCTGGGAAGCGTAA

Antitoxin

Protein

• Length: 86 a.a.
• Molecular weight: 9401.62 Da
• Isoelectric Point: 9.0330

>AT20896 WP_003381346.1 NC_004632:c19131-18874 [Pseudomonas syringae pv. tomato str. DC3000]
VANVNVRNLPDEVHRAIRIQAALHGRSTEAEIRDILERAARPEGRVKLGSFLASIAREVGGLTDKEHTLFENTRITSPAR
AVSFE

Nucleotide

• Length: 258 bp

>AT20896 NC_004632:c19131-18874 [Pseudomonas syringae pv. tomato str. DC3000]
GTGGCAAACGTGAACGTAAGAAATCTACCCGATGAAGTGCATCGGGCCATCCGCATCCAAGCTGCCCTGCACGGGCGCAG
CACCGAGGCCGAAATACGCGACATCTTGGAGCGGGCGGCGAGACCCGAGGGACGTGTGAAACTTGGCTCGTTCTTGGCGT
CTATTGCCCGCGAGGTTGGTGGTCTGACCGATAAAGAACACACCTTGTTTGAGAACACGCGCATCACGTCTCCGGCCCGT
GCGGTGAGCTTTGAATGA

Structures

Toxin

• AlphaFold DB: Q52562

Antitoxin

• AlphaFold DB: Q48B52