Detailed information of TA system TA020880

Bioinformatically predicted

Overview

TA module

• Type: II
• Classification (family/domain): vapBC/VapC-VagC
• Location: 1143628..1144262
• Replicon: chromosome
• Accession: NC_004578
• Organism: Pseudomonas syringae pv. tomato str. DC3000

Toxin (Protein)

• Gene name: vapC
• Uniprot ID: -
• Locus tag: PSPTO_RS05510
• Protein ID: WP_005770950.1
• Coordinates: 1143628..1144032 (-)
• Length: 135 a.a.

Antitoxin (Protein)

• Gene name: vapB
• Uniprot ID: Q888H8
• Locus tag: PSPTO_RS05515
• Protein ID: WP_003380366.1
• Coordinates: 1144032..1144262 (-)
• Length: 77 a.a.

Genomic Context

Locus tag	Coordinates	Strand	Size (bp)	Protein ID	Product	Description
PSPTO_RS05485	1139513..1139995	+	483	WP_002556144.1	PAS domain-containing protein	-
PSPTO_RS05490	1140091..1141347	+	1257	WP_011103393.1	3-phosphoshikimate 1-carboxyvinyltransferase	-
PSPTO_RS05495	1141370..1142032	-	663	WP_005770944.1	ChrR family anti-sigma-E factor	-
PSPTO_RS05500	1142032..1142544	-	513	WP_005615033.1	sigma-70 family RNA polymerase sigma factor	-
PSPTO_RS29855	1143178..1143444	+	267	WP_074845927.1	hypothetical protein	-
PSPTO_RS05510	1143628..1144032	-	405	WP_005770950.1	tRNA(fMet)-specific endonuclease VapC	Toxin
PSPTO_RS05515	1144032..1144262	-	231	WP_003380366.1	antitoxin	Antitoxin
PSPTO_RS05520	1144377..1145258	-	882	WP_011103395.1	aldose 1-epimerase	-
PSPTO_RS05525	1145233..1146204	-	972	WP_011103396.1	DMT family transporter	-
PSPTO_RS05530	1146288..1147568	-	1281	WP_011103397.1	TRAP transporter large permease	-
PSPTO_RS05535	1147569..1148096	-	528	WP_005770954.1	TRAP transporter small permease	-
PSPTO_RS05540	1148160..1149185	-	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: 14858.10 Da
• Isoelectric Point: 6.4779

>T20880 WP_005770950.1 NC_004578:c1144032-1143628 [Pseudomonas syringae pv. tomato str. DC3000]
MLKYMLDTNICIFTIKNKPVSVREAFNLHHGQLCISAITLMELVYGAEKSSSPERNLAVVEGFAARLELLPYDSDAAAHT
GMIRAELARAGTPIGPYDQMIAGHARSLGLVVITNNQREFQRVEGLRVEDWVSQ

Nucleotide

• Length: 405 bp

>T20880 NC_004578:c1144032-1143628 [Pseudomonas syringae pv. tomato str. DC3000]
ATGCTCAAATACATGCTCGACACCAATATCTGCATCTTCACTATCAAGAACAAGCCGGTGTCGGTACGTGAGGCCTTCAA
CCTTCATCACGGGCAGCTGTGTATCAGCGCGATCACGTTGATGGAGCTTGTCTACGGCGCAGAAAAGTCTTCCAGTCCCG
AAAGAAATCTTGCTGTTGTAGAAGGTTTTGCAGCGCGTCTTGAATTGCTTCCCTACGATAGCGACGCCGCGGCTCACACC
GGCATGATCAGAGCCGAGCTGGCCAGAGCGGGTACACCGATTGGCCCGTACGATCAAATGATTGCAGGACATGCCCGCTC
TCTTGGCCTCGTGGTCATCACCAACAACCAGCGTGAATTCCAGCGCGTCGAGGGGCTGAGGGTAGAAGACTGGGTAAGCC
AATGA

Antitoxin

Protein

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

>AT20880 WP_003380366.1 NC_004578:c1144262-1144032 [Pseudomonas syringae pv. tomato str. DC3000]
MEQSTVFKSNRSQAVRLPKAVALPDDVKRVDVVAVGRTRIISPAGEMWNSWFDGESVSDDFMAEREQPVEQLRESL

Nucleotide

• Length: 231 bp

>AT20880 NC_004578:c1144262-1144032 [Pseudomonas syringae pv. tomato str. DC3000]
ATGGAACAATCCACAGTCTTCAAAAGCAATCGAAGTCAGGCTGTTCGACTTCCAAAAGCGGTGGCATTGCCCGACGACGT
GAAACGGGTAGACGTGGTAGCAGTGGGCAGGACACGCATCATTTCCCCTGCTGGTGAAATGTGGAACAGTTGGTTCGATG
GTGAAAGTGTCAGTGATGACTTCATGGCAGAGCGCGAGCAGCCAGTTGAACAACTGCGCGAATCACTCTGA

Structures

Antitoxin

• AlphaFold DB: A0A0K8LU44