Detailed information of TA system TA055306

Bioinformatically predicted

Overview

TA module

• Type: II
• Classification (family/domain): vapBC/VapC-VagC
• Location: 5179719..5180353
• Replicon: chromosome
• Accession: NZ_CP011972
• Organism: Pseudomonas syringae pv. actinidiae ICMP 18884

Toxin (Protein)

• Gene name: vapC
• Uniprot ID: -
• Locus tag: IYO_RS23305
• Protein ID: WP_003380365.1
• Coordinates: 5179949..5180353 (+)
• Length: 135 a.a.

Antitoxin (Protein)

• Gene name: vapB
• Uniprot ID: Q888H8
• Locus tag: IYO_RS23300
• Protein ID: WP_003380366.1
• Coordinates: 5179719..5179949 (+)
• Length: 77 a.a.

Genomic Context

Locus tag	Coordinates	Strand	Size (bp)	Protein ID	Product	Description
IYO_RS23275	5174783..5175822	+	1040	Protein_4565	TRAP transporter substrate-binding protein	-
IYO_RS23280	5175886..5176413	+	528	WP_003380373.1	TRAP transporter small permease	-
IYO_RS23285	5176414..5177694	+	1281	WP_003380372.1	TRAP transporter large permease	-
IYO_RS23290	5177778..5178748	+	971	Protein_4568	DMT family transporter	-
IYO_RS23295	5178723..5179604	+	882	WP_003380368.1	aldose 1-epimerase	-
IYO_RS23300	5179719..5179949	+	231	WP_003380366.1	antitoxin	Antitoxin
IYO_RS23305	5179949..5180353	+	405	WP_003380365.1	tRNA(fMet)-specific endonuclease VapC	Toxin
IYO_RS32290	5180540..5181115	-	576	WP_019334082.1	hypothetical protein	-
IYO_RS23310	5181114..5181302	+	189	WP_003380363.1	hypothetical protein	-
IYO_RS23315	5181538..5182050	+	513	WP_003380362.1	sigma-70 family RNA polymerase sigma factor	-
IYO_RS23320	5182050..5182712	+	663	WP_003380361.1	ChrR family anti-sigma-E factor	-
IYO_RS23325	5182788..5183024	-	237	WP_003380360.1	hypothetical protein	-
IYO_RS23330	5183089..5184345	-	1257	WP_003380359.1	3-phosphoshikimate 1-carboxyvinyltransferase	-
IYO_RS23335	5184441..5184923	-	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

>T55306 WP_003380365.1 NZ_CP011972:5179949-5180353 [Pseudomonas syringae pv. actinidiae ICMP 18884]
MLKYMLDTNICIFTIKNKPVSVREAFNLHHGQLCISAITLMELVYGAEKSSSPERNLAVVEGFAARLELLPYDSAAAAHT
GMIRAELARAGTPIGPYDQMIAGHARSLGLVVITNNQREFQRVEGLRVEDWVSQ

Nucleotide

• Length: 405 bp

>T55306 NZ_CP011972:5179949-5180353 [Pseudomonas syringae pv. actinidiae ICMP 18884]
ATGCTCAAATACATGCTCGACACCAATATTTGCATCTTCACTATCAAGAACAAGCCGGTGTCGGTACGTGAGGCCTTCAA
CCTTCATCACGGGCAGCTGTGTATCAGCGCGATCACGTTGATGGAGCTTGTTTACGGCGCAGAAAAGTCTTCCAGTCCCG
AAAGAAATCTTGCTGTTGTAGAAGGTTTTGCAGCGCGTCTTGAATTGCTTCCCTACGATAGCGCCGCCGCGGCTCACACC
GGCATGATCAGAGCCGAGCTGGCCAGAGCGGGTACACCGATTGGCCCGTACGATCAAATGATTGCAGGACATGCCCGCTC
TCTTGGCCTCGTGGTCATCACCAACAACCAGCGTGAATTCCAGCGCGTCGAGGGGCTGAGGGTAGAAGACTGGGTAAGCC
AATAA

Antitoxin

Protein

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

>AT55306 WP_003380366.1 NZ_CP011972:5179719-5179949 [Pseudomonas syringae pv. actinidiae ICMP 18884]
MEQSTVFKSNRSQAVRLPKAVALPDDVKRVDVVAVGRTRIISPAGEMWNSWFDGESVSDDFMAEREQPVEQLRESL

Nucleotide

• Length: 231 bp

>AT55306 NZ_CP011972:5179719-5179949 [Pseudomonas syringae pv. actinidiae ICMP 18884]
ATGGAACAATCCACAGTCTTCAAAAGCAATCGAAGTCAGGCTGTTCGACTCCCAAAAGCGGTGGCATTACCCGACGACGT
GAAACGGGTAGACGTCGTAGCAGTGGGCAGGACACGCATCATTTCCCCTGCTGGTGAAATGTGGAACAGTTGGTTCGATG
GTGAAAGTGTCAGTGATGACTTCATGGCAGAGCGCGAGCAGCCAGTTGAACAGCTGCGCGAATCACTCTGA

Structures

Antitoxin

• AlphaFold DB: A0A0K8LU44