Detailed information of TA system TA056105

Bioinformatically predicted

Overview

TA module

• Type: II
• Classification (family/domain): vapBC/VapC-VagC
• Location: 5179722..5180356
• Replicon: chromosome
• Accession: NZ_CP012179
• Organism: Pseudomonas syringae pv. actinidiae ICMP 18708

Toxin (Protein)

• Gene name: vapC
• Uniprot ID: -
• Locus tag: NZ708_RS23310
• Protein ID: WP_003380365.1
• Coordinates: 5179952..5180356 (+)
• Length: 135 a.a.

Antitoxin (Protein)

• Gene name: vapB
• Uniprot ID: Q888H8
• Locus tag: NZ708_RS23305
• Protein ID: WP_003380366.1
• Coordinates: 5179722..5179952 (+)
• Length: 77 a.a.

Genomic Context

Locus tag	Coordinates	Strand	Size (bp)	Protein ID	Product	Description
NZ708_RS23280	5174786..5175825	+	1040	Protein_4563	TRAP transporter substrate-binding protein	-
NZ708_RS23285	5175889..5176416	+	528	WP_003380373.1	TRAP transporter small permease	-
NZ708_RS23290	5176417..5177697	+	1281	WP_003380372.1	TRAP transporter large permease	-
NZ708_RS23295	5177781..5178751	+	971	Protein_4566	DMT family transporter	-
NZ708_RS23300	5178726..5179607	+	882	WP_003380368.1	aldose 1-epimerase	-
NZ708_RS23305	5179722..5179952	+	231	WP_003380366.1	antitoxin	Antitoxin
NZ708_RS23310	5179952..5180356	+	405	WP_003380365.1	tRNA(fMet)-specific endonuclease VapC	Toxin
NZ708_RS32280	5180543..5181118	-	576	WP_019334082.1	hypothetical protein	-
NZ708_RS23315	5181117..5181305	+	189	WP_003380363.1	hypothetical protein	-
NZ708_RS23320	5181541..5182053	+	513	WP_003380362.1	sigma-70 family RNA polymerase sigma factor	-
NZ708_RS23325	5182053..5182715	+	663	WP_003380361.1	ChrR family anti-sigma-E factor	-
NZ708_RS23330	5182791..5183027	-	237	WP_003380360.1	hypothetical protein	-
NZ708_RS23335	5183092..5184348	-	1257	WP_003380359.1	3-phosphoshikimate 1-carboxyvinyltransferase	-
NZ708_RS23340	5184444..5184926	-	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)
	-	inside	Genomic island	-	-	5170667..5181118	10451

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

>T56105 WP_003380365.1 NZ_CP012179:5179952-5180356 [Pseudomonas syringae pv. actinidiae ICMP 18708]
MLKYMLDTNICIFTIKNKPVSVREAFNLHHGQLCISAITLMELVYGAEKSSSPERNLAVVEGFAARLELLPYDSAAAAHT
GMIRAELARAGTPIGPYDQMIAGHARSLGLVVITNNQREFQRVEGLRVEDWVSQ

Nucleotide

• Length: 405 bp

>T56105 NZ_CP012179:5179952-5180356 [Pseudomonas syringae pv. actinidiae ICMP 18708]
ATGCTCAAATACATGCTCGACACCAATATTTGCATCTTCACTATCAAGAACAAGCCGGTGTCGGTACGTGAGGCCTTCAA
CCTTCATCACGGGCAGCTGTGTATCAGCGCGATCACGTTGATGGAGCTTGTTTACGGCGCAGAAAAGTCTTCCAGTCCCG
AAAGAAATCTTGCTGTTGTAGAAGGTTTTGCAGCGCGTCTTGAATTGCTTCCCTACGATAGCGCCGCCGCGGCTCACACC
GGCATGATCAGAGCCGAGCTGGCCAGAGCGGGTACACCGATTGGCCCGTACGATCAAATGATTGCAGGACATGCCCGCTC
TCTTGGCCTCGTGGTCATCACCAACAACCAGCGTGAATTCCAGCGCGTCGAGGGGCTGAGGGTAGAAGACTGGGTAAGCC
AATAA

Antitoxin

Protein

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

>AT56105 WP_003380366.1 NZ_CP012179:5179722-5179952 [Pseudomonas syringae pv. actinidiae ICMP 18708]
MEQSTVFKSNRSQAVRLPKAVALPDDVKRVDVVAVGRTRIISPAGEMWNSWFDGESVSDDFMAEREQPVEQLRESL

Nucleotide

• Length: 231 bp

>AT56105 NZ_CP012179:5179722-5179952 [Pseudomonas syringae pv. actinidiae ICMP 18708]
ATGGAACAATCCACAGTCTTCAAAAGCAATCGAAGTCAGGCTGTTCGACTCCCAAAAGCGGTGGCATTACCCGACGACGT
GAAACGGGTAGACGTCGTAGCAGTGGGCAGGACACGCATCATTTCCCCTGCTGGTGAAATGTGGAACAGTTGGTTCGATG
GTGAAAGTGTCAGTGATGACTTCATGGCAGAGCGCGAGCAGCCAGTTGAACAGCTGCGCGAATCACTCTGA

Structures

Antitoxin

• AlphaFold DB: A0A0K8LU44