Detailed information of TA system TA023528

Bioinformatically predicted

Overview

TA module

• Type: II
• Classification (family/domain): vapBC/VapC-VagC
• Location: 1244227..1244894
• Replicon: chromosome
• Accession: NC_011989
• Organism: Agrobacterium vitis S4

Toxin (Protein)

• Gene name: vapC
• Uniprot ID: -
• Locus tag: AVI_RS05825
• Protein ID: WP_015915484.1
• Coordinates: 1244227..1244652 (-)
• Length: 142 a.a.

Antitoxin (Protein)

• Gene name: vapB
• Uniprot ID: B9JUR6
• Locus tag: AVI_RS05830
• Protein ID: WP_015915485.1
• Coordinates: 1244649..1244894 (-)
• Length: 82 a.a.

Genomic Context

Locus tag	Coordinates	Strand	Size (bp)	Protein ID	Product	Description
AVI_RS05800	1240182..1241798	-	1617	WP_015915479.1	citramalate synthase	-
AVI_RS05805	1241822..1242787	-	966	WP_015915480.1	prolyl aminopeptidase	-
AVI_RS05810	1242780..1243274	-	495	WP_015915481.1	GFA family protein	-
AVI_RS05815	1243271..1243738	-	468	WP_015915482.1	GFA family protein	-
AVI_RS05820	1243735..1244223	-	489	WP_015915483.1	GFA family protein	-
AVI_RS05825	1244227..1244652	-	426	WP_015915484.1	type II toxin-antitoxin system VapC family toxin	Toxin
AVI_RS05830	1244649..1244894	-	246	WP_015915485.1	AbrB/MazE/SpoVT family DNA-binding domain-containing protein	Antitoxin
AVI_RS05835	1244985..1245374	-	390	WP_015915486.1	VOC family protein	-
AVI_RS05840	1245504..1247144	-	1641	WP_041696391.1	cysteine--tRNA ligase	-
AVI_RS05845	1247490..1249124	+	1635	WP_015915488.1	glycoside hydrolase family 28 protein	-
AVI_RS05850	1249308..1249871	+	564	WP_015915489.1	dTDP-4-dehydrorhamnose 3,5-epimerase	-

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 (6-126)

Antitoxin

• SpoVT-AbrB domain (10-58)

Sequences

Toxin

Protein

• Length: 142 a.a.
• Molecular weight: 15660.03 Da
• Isoelectric Point: 5.6153

>T23528 WP_015915484.1 NC_011989:c1244652-1244227 [Agrobacterium vitis S4]
MITARYMLDTNIISDVVRNPMGRAADVMHGLNRDDICLSSIVLSEILFGIQRKGSERLTRLVEGVLERIAVIAYDDLAGR
HYAEIRTALEKQGTPIGATDLFIAAHALSLDMVLVTNNTREFARVPGLKLENWLETAHEGQ

Nucleotide

• Length: 426 bp

>T23528 NC_011989:c1244652-1244227 [Agrobacterium vitis S4]
ATGATAACCGCGCGCTACATGCTCGACACCAATATTATCTCTGATGTGGTGCGAAATCCTATGGGCAGGGCGGCAGACGT
TATGCATGGCCTCAACCGTGACGATATTTGCCTGAGTTCAATTGTTCTGTCGGAAATCCTGTTTGGCATACAGCGCAAAG
GCTCCGAGCGGCTTACTCGTCTGGTTGAAGGGGTCTTGGAAAGGATCGCTGTCATTGCCTATGATGATTTGGCGGGCCGT
CATTATGCTGAGATTCGCACCGCCTTGGAAAAACAGGGAACACCTATCGGCGCAACCGACCTGTTCATCGCCGCCCACGC
GCTGTCGCTGGATATGGTTCTGGTCACCAACAATACCCGTGAATTTGCCCGCGTACCCGGGCTGAAACTGGAAAACTGGC
TCGAAACCGCACATGAGGGACAATAG

Antitoxin

Protein

• Length: 82 a.a.
• Molecular weight: 9677.04 Da
• Isoelectric Point: 4.5837

>AT23528 WP_015915485.1 NC_011989:c1244894-1244649 [Agrobacterium vitis S4]
MEQERHVRVFKNGRNRAVRIPVEFEFPGDEVIMRKEGDRIIIEPVNDKKQNLIEWLRSQPPIEEDFPDFDLIEPPPRPVD
L

Nucleotide

• Length: 246 bp

>AT23528 NC_011989:c1244894-1244649 [Agrobacterium vitis S4]
ATGGAGCAGGAAAGACATGTGCGGGTGTTCAAGAACGGTCGCAATCGCGCCGTCCGCATCCCCGTGGAATTCGAGTTTCC
GGGCGATGAAGTGATCATGCGCAAGGAAGGCGACCGGATCATTATTGAGCCTGTCAACGACAAGAAGCAAAATCTGATCG
AGTGGCTGCGCAGTCAGCCGCCTATCGAGGAGGATTTTCCCGATTTTGATCTGATTGAACCACCGCCGAGACCAGTCGAT
CTATGA

Structures

Antitoxin

• AlphaFold DB: B9JUR6