Detailed information of TA system TA073402

Bioinformatically predicted

Overview

TA module

• Type: II
• Classification (family/domain): vapBC/VapC-VagC
• Location: 1197208..1197842
• Replicon: chromosome
• Accession: NZ_CP019871
• Organism: Pseudomonas syringae pv. tomato strain B13-200

Toxin (Protein)

• Gene name: vapC
• Uniprot ID: -
• Locus tag: XJ28_RS06115
• Protein ID: WP_003380365.1
• Coordinates: 1197208..1197612 (-)
• Length: 135 a.a.

Antitoxin (Protein)

• Gene name: vapB
• Uniprot ID: Q888H8
• Locus tag: XJ28_RS06120
• Protein ID: WP_003380366.1
• Coordinates: 1197612..1197842 (-)
• Length: 77 a.a.

Genomic Context

Locus tag	Coordinates	Strand	Size (bp)	Protein ID	Product	Description
XJ28_RS06085	1193094..1193576	+	483	WP_002556144.1	PAS domain-containing protein	-
XJ28_RS06090	1193672..1194928	+	1257	WP_007244165.1	3-phosphoshikimate 1-carboxyvinyltransferase	-
XJ28_RS06095	1194950..1195612	-	663	WP_005770944.1	ChrR family anti-sigma-E factor	-
XJ28_RS06100	1195612..1196124	-	513	WP_005615033.1	sigma-70 family RNA polymerase sigma factor	-
XJ28_RS32440	1196758..1197024	+	267	WP_074845927.1	hypothetical protein	-
XJ28_RS06115	1197208..1197612	-	405	WP_003380365.1	tRNA(fMet)-specific endonuclease VapC	Toxin
XJ28_RS06120	1197612..1197842	-	231	WP_003380366.1	antitoxin	Antitoxin
XJ28_RS06125	1197956..1198837	-	882	WP_007244162.1	aldose 1-epimerase	-
XJ28_RS06130	1198812..1199783	-	972	WP_007244161.1	DMT family transporter	-
XJ28_RS06135	1199867..1201147	-	1281	WP_005736622.1	TRAP transporter large permease	-
XJ28_RS06140	1201148..1201675	-	528	WP_005770954.1	TRAP transporter small permease	-
XJ28_RS06145	1201739..1202764	-	1026	WP_005770956.1	TRAP transporter substrate-binding protein	-

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 (4-124)

Antitoxin

• SpoVT-AbrB domain (7-34)

Sequences

Toxin

Protein

• Length: 135 a.a.
• Molecular weight: 14814.09 Da
• Isoelectric Point: 6.8615

>T73402 WP_003380365.1 NZ_CP019871:c1197612-1197208 [Pseudomonas syringae pv. tomato]
MLKYMLDTNICIFTIKNKPVSVREAFNLHHGQLCISAITLMELVYGAEKSSSPERNLAVVEGFAARLELLPYDSAAAAHT
GMIRAELARAGTPIGPYDQMIAGHARSLGLVVITNNQREFQRVEGLRVEDWVSQ

Nucleotide

• Length: 405 bp

>T73402 NZ_CP019871:c1197612-1197208 [Pseudomonas syringae pv. tomato]
ATGCTCAAATACATGCTCGACACCAATATCTGCATCTTCACTATCAAGAACAAGCCGGTGTCGGTACGTGAGGCCTTCAA
CCTTCATCACGGGCAGCTGTGTATCAGCGCGATCACGTTGATGGAGCTTGTCTACGGCGCAGAAAAGTCTTCCAGCCCCG
AAAGAAATCTTGCTGTTGTAGAAGGTTTTGCAGCGCGTCTTGAATTGCTTCCCTACGATAGCGCCGCCGCGGCTCACACC
GGCATGATCAGAGCCGAGCTGGCCAGAGCGGGTACACCGATTGGCCCGTACGATCAAATGATTGCAGGACATGCCCGCTC
TCTTGGCCTCGTGGTCATCACCAACAACCAGCGTGAATTCCAGCGCGTCGAGGGGCTGAGGGTAGAAGACTGGGTAAGCC
AATGA

Antitoxin

Protein

• Length: 77 a.a.
• Molecular weight: 8593.67 Da
• Isoelectric Point: 4.5557

>AT73402 WP_003380366.1 NZ_CP019871:c1197842-1197612 [Pseudomonas syringae pv. tomato]
MEQSTVFKSNRSQAVRLPKAVALPDDVKRVDVVAVGRTRIISPAGEMWNSWFDGESVSDDFMAEREQPVEQLRESL

Nucleotide

• Length: 231 bp

>AT73402 NZ_CP019871:c1197842-1197612 [Pseudomonas syringae pv. tomato]
ATGGAACAATCCACAGTCTTCAAAAGCAATCGAAGTCAGGCTGTTCGACTTCCAAAAGCGGTGGCATTGCCCGACGACGT
GAAACGGGTAGACGTCGTAGCAGTGGGCAGGACACGCATCATTTCCCCTGCTGGTGAAATGTGGAACAGTTGGTTCGATG
GTGAAAGTGTCAGTGATGACTTCATGGCAGAGCGCGAGCAGCCAGTTGAACAACTGCGCGAATCACTCTGA

Structures

Antitoxin

• AlphaFold DB: A0A0K8LU44