Detailed information of TA system TA058476

Bioinformatically predicted

Overview

TA module

• Type: II
• Classification (family/domain): vagCD/VapC-VagC
• Location: 41869..42512
• Replicon: plasmid pKPYL2
• Accession: NZ_CP013340
• Organism: Raoultella ornithinolytica strain Yangling I2

Toxin (Protein)

• Gene name: vagD
• Uniprot ID: A0A5P6KDG5
• Locus tag: ATN83_RS26470
• Protein ID: WP_021312768.1
• Coordinates: 41869..42285 (-)
• Length: 139 a.a.

Antitoxin (Protein)

• Gene name: vagC
• Uniprot ID: A0A5P6KGW8
• Locus tag: ATN83_RS26475
• Protein ID: WP_021312767.1
• Coordinates: 42282..42512 (-)
• Length: 77 a.a.

Genomic Context

Locus tag	Coordinates	Strand	Size (bp)	Protein ID	Product	Description
ATN83_RS26445	38033..38497	+	465	WP_001243598.1	isoprenylcysteine carboxylmethyltransferase family protein	-
ATN83_RS26450	38777..39301	-	525	Protein_37	IS5-like element ISKpn26 family transposase	-
ATN83_RS26455	39337..40776	-	1440	Protein_38	IS66 family transposase	-
ATN83_RS26460	40841..41545	+	705	WP_001067855.1	IS6-like element IS26 family transposase	-
ATN83_RS26465	41631..41771	+	141	WP_045286941.1	helix-turn-helix domain-containing protein	-
ATN83_RS26470	41869..42285	-	417	WP_021312768.1	type II toxin-antitoxin system VapC family toxin	Toxin
ATN83_RS26475	42282..42512	-	231	WP_021312767.1	AbrB/MazE/SpoVT family DNA-binding domain-containing protein	Antitoxin
ATN83_RS28790	42566..42970	+	405	Protein_43	hypothetical protein	-
ATN83_RS26485	43140..43358	+	219	WP_006788213.1	type II toxin-antitoxin system antitoxin CcdA	-
ATN83_RS26490	43360..43665	+	306	WP_006788214.1	type II toxin-antitoxin system toxin CcdB	-
ATN83_RS28655	44351..44836	+	486	Protein_46	hypothetical protein	-
ATN83_RS26500	45072..45866	+	795	WP_016240356.1	site-specific integrase	-
ATN83_RS28360	46306..46485	-	180	WP_006788217.1	hypothetical protein	-
ATN83_RS26505	46605..47231	-	627	WP_016946792.1	ParA family plasmid-partitioning AAA ATPase	-

Associated MGEs

MGE detail	Similar MGEs	Relative position	MGE Type	Cargo ARG	Virulence gene	Coordinates	Length (bp)
	-	inside	Conjugative plasmid	-	-	1..140936	140936

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 (5-129)

Antitoxin

• SpoVT-AbrB domain (7-50)

Sequences

Toxin

Protein

• Length: 139 a.a.
• Molecular weight: 15175.60 Da
• Isoelectric Point: 7.2452

>T58476 WP_021312768.1 NZ_CP013340:c42285-41869 [Raoultella ornithinolytica]
VNKIYMLDTNICSFIMREQPEAVLKRLEQAVLRGHRIVVSAITYSEMRFGATGPKASPRHVQLVDAFCARLDAILPWDRA
AVDATTEIKVALRLAGTPIGPNDTAIAGHAIAAGAVLVTNNVREFERVPDLVLEDWVR

Nucleotide

• Length: 417 bp

>T58476 NZ_CP013340:c42285-41869 [Raoultella ornithinolytica]
GTGAACAAGATCTATATGCTCGACACCAACATCTGCTCGTTCATCATGCGCGAGCAGCCTGAAGCGGTGCTGAAGCGCCT
GGAGCAGGCGGTGCTGCGTGGCCACCGTATCGTGGTCTCGGCCATCACTTATTCTGAAATGCGCTTCGGTGCCACCGGCC
CGAAGGCCTCGCCGCGCCACGTCCAGCTGGTCGACGCGTTCTGCGCCCGCCTCGATGCCATCCTGCCCTGGGACCGCGCT
GCGGTGGACGCCACCACGGAGATTAAGGTGGCGCTGCGCCTCGCCGGAACGCCGATAGGCCCGAACGACACGGCGATCGC
CGGGCATGCCATTGCGGCCGGCGCCGTACTGGTGACAAATAATGTGCGGGAGTTTGAGCGGGTGCCGGATCTGGTGCTGG
AAGACTGGGTAAGATAA

Antitoxin

Protein

• Length: 77 a.a.
• Molecular weight: 8722.81 Da
• Isoelectric Point: 4.4692

>AT58476 WP_021312767.1 NZ_CP013340:c42512-42282 [Raoultella ornithinolytica]
MRTVSIFKNGNNRAIRLPRDLDFEGVSELEIVREGDSIILRPVRPTWGSFAQLEKADPDFMAEREDVVSDEGRFNL

Nucleotide

• Length: 231 bp

>AT58476 NZ_CP013340:c42512-42282 [Raoultella ornithinolytica]
ATGAGAACCGTATCTATTTTTAAAAACGGCAACAACCGCGCCATCCGCCTTCCCCGCGATCTGGATTTTGAGGGGGTGAG
CGAGCTGGAGATCGTCCGGGAAGGGGACAGCATCATCCTGCGTCCCGTCCGGCCGACCTGGGGGTCGTTCGCGCAGCTCG
AAAAAGCCGATCCGGACTTTATGGCGGAGCGCGAGGACGTTGTCAGCGACGAAGGAAGATTTAACCTGTGA

Structures

Toxin

• AlphaFold DB: A0A5P6KDG5

Antitoxin

• AlphaFold DB: A0A5P6KGW8