Detailed information of TA system TA112038

Bioinformatically predicted

Overview

TA module

• Type: II
• Classification (family/domain): vapBC/VapC-VagC
• Location: 5370804..5371438
• Replicon: chromosome
• Accession: NZ_CP032631
• Organism: Pseudomonas syringae pv. actinidiae str. Shaanxi_M228

Toxin (Protein)

• Gene name: vapC
• Uniprot ID: -
• Locus tag: CN228_RS26075
• Protein ID: WP_003380365.1
• Coordinates: 5371034..5371438 (+)
• Length: 135 a.a.

Antitoxin (Protein)

• Gene name: vapB
• Uniprot ID: Q888H8
• Locus tag: CN228_RS26070
• Protein ID: WP_003380366.1
• Coordinates: 5370804..5371034 (+)
• Length: 77 a.a.

Genomic Context

Locus tag	Coordinates	Strand	Size (bp)	Protein ID	Product	Description
CN228_RS26045	5365876..5366907	+	1032	WP_020312848.1	TRAP transporter substrate-binding protein	-
CN228_RS26050	5366971..5367498	+	528	WP_003380373.1	TRAP transporter small permease	-
CN228_RS26055	5367499..5368779	+	1281	WP_003380372.1	TRAP transporter large permease	-
CN228_RS26060	5368863..5369833	+	971	Protein_4741	DMT family transporter	-
CN228_RS26065	5369808..5370689	+	882	WP_003380368.1	aldose 1-epimerase	-
CN228_RS26070	5370804..5371034	+	231	WP_003380366.1	antitoxin	Antitoxin
CN228_RS26075	5371034..5371438	+	405	WP_003380365.1	tRNA(fMet)-specific endonuclease VapC	Toxin
CN228_RS26080	5371625..5372200	-	576	WP_003380364.1	hypothetical protein	-
CN228_RS26085	5372199..5372387	+	189	WP_003380363.1	hypothetical protein	-
CN228_RS26090	5372623..5373135	+	513	WP_003380362.1	sigma-70 family RNA polymerase sigma factor	-
CN228_RS26095	5373135..5373797	+	663	WP_003380361.1	ChrR family anti-sigma-E factor	-
CN228_RS26100	5373873..5374109	-	237	WP_003380360.1	hypothetical protein	-
CN228_RS26105	5374174..5375430	-	1257	WP_003380359.1	3-phosphoshikimate 1-carboxyvinyltransferase	-
CN228_RS26110	5375526..5376008	-	483	WP_003380358.1	PAS domain-containing 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

>T112038 WP_003380365.1 NZ_CP032631:5371034-5371438 [Pseudomonas syringae pv. actinidiae str. Shaanxi_M228]
MLKYMLDTNICIFTIKNKPVSVREAFNLHHGQLCISAITLMELVYGAEKSSSPERNLAVVEGFAARLELLPYDSAAAAHT
GMIRAELARAGTPIGPYDQMIAGHARSLGLVVITNNQREFQRVEGLRVEDWVSQ

Nucleotide

• Length: 405 bp

>T112038 NZ_CP032631:5371034-5371438 [Pseudomonas syringae pv. actinidiae str. Shaanxi_M228]
ATGCTCAAATACATGCTCGACACCAATATTTGCATCTTCACTATCAAGAACAAGCCGGTGTCGGTACGTGAGGCCTTCAA
CCTTCATCACGGGCAGCTGTGTATCAGCGCGATCACGTTGATGGAGCTTGTTTACGGCGCAGAAAAGTCTTCCAGTCCCG
AAAGAAATCTTGCTGTTGTAGAAGGTTTTGCAGCGCGTCTTGAATTGCTTCCCTACGATAGCGCCGCCGCGGCTCACACC
GGCATGATCAGAGCCGAGCTGGCCAGAGCGGGTACACCGATTGGCCCGTACGATCAAATGATTGCAGGACATGCCCGCTC
TCTTGGCCTCGTGGTCATCACCAACAACCAGCGTGAATTCCAGCGCGTCGAGGGGCTGAGGGTAGAAGACTGGGTAAGCC
AATAA

Antitoxin

Protein

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

>AT112038 WP_003380366.1 NZ_CP032631:5370804-5371034 [Pseudomonas syringae pv. actinidiae str. Shaanxi_M228]
MEQSTVFKSNRSQAVRLPKAVALPDDVKRVDVVAVGRTRIISPAGEMWNSWFDGESVSDDFMAEREQPVEQLRESL

Nucleotide

• Length: 231 bp

>AT112038 NZ_CP032631:5370804-5371034 [Pseudomonas syringae pv. actinidiae str. Shaanxi_M228]
ATGGAACAATCCACAGTCTTCAAAAGCAATCGAAGTCAGGCTGTTCGACTCCCAAAAGCGGTGGCATTACCCGACGACGT
GAAACGGGTAGACGTCGTAGCAGTGGGCAGGACACGCATCATTTCCCCTGCTGGTGAAATGTGGAACAGTTGGTTCGATG
GTGAAAGTGTCAGTGATGACTTCATGGCAGAGCGCGAGCAGCCAGTTGAACAGCTGCGCGAATCACTCTGA

Structures

Antitoxin

• AlphaFold DB: A0A0K8LU44