Detailed information of TA system TA107258

Bioinformatically predicted

Overview

TA module

• Type: II
• Classification (family/domain): vapBC/VapC-VagC
• Location: 2328956..2329614
• Replicon: chromosome
• Accession: NZ_CP030164
• Organism: Xanthomonas citri pv. punicae strain LMG7439

Toxin (Protein)

• Gene name: vapC
• Uniprot ID: Q8PRH3
• Locus tag: XapA_RS10350
• Protein ID: WP_011053002.1
• Coordinates: 2329213..2329614 (+)
• Length: 134 a.a.

Antitoxin (Protein)

• Gene name: vapB
• Uniprot ID: Q3C002
• Locus tag: XapA_RS10345
• Protein ID: WP_005917852.1
• Coordinates: 2328956..2329216 (+)
• Length: 87 a.a.

Genomic Context

Locus tag	Coordinates	Strand	Size (bp)	Protein ID	Product	Description
XapA_RS10330	2325083..2328271	+	3189	WP_174854877.1	TAL effector repeat-containing protein	-
XapA_RS10335	2328382..2328765	-	384	Protein_1930	recombinase family protein	-
XapA_RS10345	2328956..2329216	+	261	WP_005917852.1	AbrB/MazE/SpoVT family DNA-binding domain-containing protein	Antitoxin
XapA_RS10350	2329213..2329614	+	402	WP_011053002.1	type II toxin-antitoxin system VapC family toxin	Toxin
XapA_RS10355	2329639..2329902	+	264	WP_005917846.1	hypothetical protein	-
XapA_RS10360	2329909..2330139	+	231	Protein_1934	zeta toxin family protein	-
XapA_RS10365	2330163..2331539	-	1377	WP_160964032.1	IS5 family transposase	-
XapA_RS10370	2331657..2332805	+	1149	Protein_1936	type VI secretion protein	-
XapA_RS10375	2332802..2333470	+	669	WP_005934603.1	hypothetical protein	-
XapA_RS10380	2333518..2333730	+	213	WP_005934599.1	hypothetical protein	-
XapA_RS10385	2333723..2333911	+	189	Protein_1939	hypothetical protein	-

Associated MGEs

MGE detail	Similar MGEs	Relative position	MGE Type	Cargo ARG	Virulence gene	Coordinates	Length (bp)
	-	inside	Genomic island	-	-	2328956..2337311	8355
	-	inside	IScluster/Tn	-	-	2328337..2344180	15843

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 (4-122)

Antitoxin

• SpoVT-AbrB domain (8-52)

Sequences

Toxin

Protein

• Length: 134 a.a.
• Molecular weight: 14627.05 Da
• Isoelectric Point: 7.2785

>T107258 WP_011053002.1 NZ_CP030164:2329213-2329614 [Xanthomonas citri pv. punicae]
MKRYMLDTNTVSHLVKSHPAVSRRVIEVPMTALCMSAITGGELMFGLAKVPDAKRLQQAVMELLRRVDVLPWDGAVMERY
GSVRADLEKQGKALGSLDMLIAAHALETDSVLVTNDAAFSRVVGLTVEDWTRS

Nucleotide

• Length: 402 bp

>T107258 NZ_CP030164:2329213-2329614 [Xanthomonas citri pv. punicae]
ATGAAGCGGTACATGCTTGATACCAACACCGTGAGCCATCTCGTCAAGAGCCATCCCGCTGTCTCTCGACGGGTCATTGA
AGTGCCTATGACTGCGCTATGTATGTCCGCAATTACCGGTGGGGAGCTGATGTTCGGCTTGGCTAAGGTGCCAGACGCCA
AACGCCTTCAGCAAGCCGTCATGGAACTCCTGCGGCGCGTGGATGTGCTGCCTTGGGATGGCGCGGTAATGGAGCGTTAC
GGAAGCGTGAGAGCGGACCTAGAAAAGCAAGGTAAAGCGCTTGGGTCGCTCGACATGCTTATCGCAGCACATGCACTGGA
AACGGATTCTGTCCTCGTTACCAATGACGCCGCATTTAGTCGTGTTGTTGGTTTGACCGTGGAAGATTGGACACGCAGCT
AA

Antitoxin

Protein

• Length: 87 a.a.
• Molecular weight: 9770.95 Da
• Isoelectric Point: 5.0941

>AT107258 WP_005917852.1 NZ_CP030164:2328956-2329216 [Xanthomonas citri pv. punicae]
VSQVAKLFINGRSQAVRLPAAYRFTEKEVFIRQDPETGDVILSRKPATWEDFFIALKSADVPANFLDAAERNQGTQDRDP
FAGWRE

Nucleotide

• Length: 261 bp

>AT107258 NZ_CP030164:2328956-2329216 [Xanthomonas citri pv. punicae]
GTGAGCCAAGTTGCCAAGCTGTTCATCAATGGCCGCAGCCAGGCAGTCCGCTTGCCTGCCGCCTATCGCTTTACCGAGAA
AGAGGTTTTCATTCGCCAAGACCCGGAGACCGGTGACGTCATCCTGTCTCGGAAGCCTGCAACGTGGGAGGACTTCTTTA
TCGCACTCAAGAGCGCAGATGTGCCTGCTAATTTTCTAGATGCCGCCGAGCGCAATCAGGGCACGCAGGACCGTGATCCT
TTTGCGGGATGGCGCGAATGA

Structures

Toxin

• AlphaFold DB: Q8PRH3

Antitoxin

• AlphaFold DB: Q3C002