Detailed information of TA system TA024520

Bioinformatically predicted

Overview

TA module

• Type: II
• Classification (family/domain): vagCD/VapC-VagC
• Location: 33519..34168
• Replicon: plasmid pCROD1
• Accession: NC_013717
• Organism: Citrobacter rodentium ICC168

Toxin (Protein)

• Gene name: vagD
• Uniprot ID: D2TV52
• Locus tag: ROD_RS25160
• Protein ID: WP_012908926.1
• Coordinates: 33519..33941 (-)
• Length: 141 a.a.

Antitoxin (Protein)

• Gene name: vagC
• Uniprot ID: D2TV53
• Locus tag: ROD_RS25165
• Protein ID: WP_012908927.1
• Coordinates: 33938..34168 (-)
• Length: 77 a.a.

Genomic Context

Locus tag	Coordinates	Strand	Size (bp)	Protein ID	Product	Description
ROD_RS25155	30578..31048	+	471	WP_012908923.1	hypothetical protein	-
ROD_RS27870	31572..32285	+	714	WP_148222154.1	hypothetical protein	-
ROD_RS28565	32617..32847	-	231	WP_148222155.1	hypothetical protein	-
ROD_RS25160	33519..33941	-	423	WP_012908926.1	type II toxin-antitoxin system VapC family toxin	Toxin
ROD_RS25165	33938..34168	-	231	WP_012908927.1	AbrB/MazE/SpoVT family DNA-binding domain-containing protein	Antitoxin
ROD_RS25170	34837..35055	+	219	WP_012908929.1	type II toxin-antitoxin system antitoxin CcdA	-
ROD_RS25175	35057..35362	+	306	WP_012908930.1	type II toxin-antitoxin system toxin CcdB	-
ROD_RS25180	35364..35690	+	327	WP_024133139.1	hypothetical protein	-
ROD_RS25185	35680..36471	+	792	WP_012908932.1	site-specific integrase	-

Associated MGEs

MGE detail	Similar MGEs	Relative position	MGE Type	Cargo ARG	Virulence gene	Coordinates	Length (bp)
	-	inside	Non-Mobilizable plasmid	-	pic	1..54449	54449

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 (7-48)

Sequences

Toxin

Protein

• Length: 141 a.a.
• Molecular weight: 15334.77 Da
• Isoelectric Point: 8.5291

>T24520 WP_012908926.1 NC_013717:c33941-33519 [Citrobacter rodentium ICC168]
MKKTYMLDTNICSFIMREQPEAVLKRLEQAVLRGHRIVVSAITYAEMRFGATGLKASTRHVQLVDAFCARLDAILPWDRA
AADATTDIRVVLRLAGTPLGPNDTAIAGHAIASGAILVTNNVREFERVPGLMQEDWGKTG

Nucleotide

• Length: 423 bp

>T24520 NC_013717:c33941-33519 [Citrobacter rodentium ICC168]
ATGAAGAAAACCTATATGCTCGACACTAACATCTGCTCGTTCATCATGCGCGAGCAGCCGGAAGCCGTGCTGAAGCGCCT
GGAGCAGGCGGTGCTGCGTGGTCACCGCATCGTGGTATCAGCCATTACCTATGCGGAAATGCGTTTCGGTGCCACCGGCC
TGAAGGCCTCAACGCGTCATGTTCAGCTGGTCGACGCGTTCTGTGCGCGGCTCGATGCCATCCTGCCCTGGGACCGCGCC
GCAGCGGACGCCACAACGGACATCAGGGTGGTGCTGCGCCTCGCCGGGACACCGCTCGGTCCGAACGACACGGCCATTGC
CGGACACGCCATCGCGTCAGGAGCAATTCTGGTGACGAATAATGTGAGAGAGTTTGAGCGGGTGCCGGGCCTGATGCAGG
AAGACTGGGGTAAAACAGGATAG

Antitoxin

Protein

• Length: 77 a.a.
• Molecular weight: 8741.77 Da
• Isoelectric Point: 4.3654

>AT24520 WP_012908927.1 NC_013717:c34168-33938 [Citrobacter rodentium ICC168]
MRTVSIFKNGNNRAIRLPRDLDFEGVSELEIVREGDSIILRPVRPTWGSFAQLDRADTDFMAEREDVVSDEGRFEV

Nucleotide

• Length: 231 bp

>AT24520 NC_013717:c34168-33938 [Citrobacter rodentium ICC168]
ATGAGAACCGTATCCATTTTTAAAAATGGTAACAACCGCGCCATTCGTCTGCCCCGTGATCTGGATTTTGAGGGCGTCAG
CGAGCTGGAGATCGTCCGGGAAGGGGACAGCATCATTCTGCGTCCCGTCCGGCCGACCTGGGGTTCGTTCGCGCAGCTGG
ACAGGGCCGATACGGACTTTATGGCGGAGCGTGAGGACGTGGTCAGCGATGAAGGACGTTTTGAGGTATGA

Structures

Toxin

• AlphaFold DB: D2TV52

Antitoxin

• AlphaFold DB: D2TV53