Detailed information of TA system TA024512

Bioinformatically predicted

Overview

TA module

• Type: II
• Classification (family/domain): vapBC/LOTUS_5_Limkain_b1(toxin)
• Location: 4075748..4076364
• Replicon: chromosome
• Accession: NC_013716
• Organism: Citrobacter rodentium ICC168

Toxin (Protein)

• Gene name: vapC
• Uniprot ID: D2TUA6
• Locus tag: ROD_RS19115
• Protein ID: WP_012907852.1
• Coordinates: 4075748..4076122 (-)
• Length: 125 a.a.

Antitoxin (Protein)

• Gene name: vapB
• Uniprot ID: -
• Locus tag: ROD_RS19120
• Protein ID: WP_162467731.1
• Coordinates: 4076122..4076364 (-)
• Length: 81 a.a.

Genomic Context

Locus tag	Coordinates	Strand	Size (bp)	Protein ID	Product	Description
ROD_RS19100	4072986..4073888	+	903	WP_012907849.1	formate dehydrogenase subunit beta	-
ROD_RS19105	4073885..4074520	+	636	WP_012907850.1	formate dehydrogenase cytochrome b556 subunit	-
ROD_RS19110	4074781..4075710	+	930	WP_012907851.1	formate dehydrogenase accessory protein FdhE	-
ROD_RS19115	4075748..4076122	-	375	WP_012907852.1	type II toxin-antitoxin system VapC family toxin	Toxin
ROD_RS19120	4076122..4076364	-	243	WP_162467731.1	ribbon-helix-helix domain-containing protein	Antitoxin
ROD_RS19125	4076630..4077337	+	708	WP_012904922.1	T3SS effector protein NleD	-
ROD_RS19130	4077371..4078591	+	1221	WP_012907853.1	ISL3 family transposase	-
ROD_RS19135	4078647..4079588	+	942	WP_012907854.1	alpha/beta hydrolase	-
ROD_RS19140	4079598..4080539	-	942	WP_024132973.1	fatty acid biosynthesis protein FabY	-
ROD_RS19145	4080584..4081021	-	438	WP_012907856.1	D-tyrosyl-tRNA(Tyr) deacylase	-

Associated MGEs

MGE detail	Similar MGEs	Relative position	MGE Type	Cargo ARG	Virulence gene	Coordinates	Length (bp)
	-	flank	IS/Tn	-	-	4077371..4078591	1220

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 (6-110)

Antitoxin

• Ribbon-helix-helix protein, CopG (13-47)

Sequences

Toxin

Protein

• Length: 125 a.a.
• Molecular weight: 14010.40 Da
• Isoelectric Point: 9.5229

>T24512 WP_012907852.1 NC_013716:c4076122-4075748 [Citrobacter rodentium ICC168]
MRRVPVLFDTNILIDLFSGRIEAKQALETYPPQNAISLITWMEVMVGAKKYHQENRTRIALNAFNVIGVTQEIAERSVSL
RQVYGMKLPDAIILATAQIHRCELVTRNTKDFAGLPGVIIPYNL

Nucleotide

• Length: 375 bp

>T24512 NC_013716:c4076122-4075748 [Citrobacter rodentium ICC168]
ATGCGCCGGGTACCCGTACTATTTGACACTAATATTCTGATCGATTTATTCAGTGGACGTATTGAAGCGAAACAAGCGCT
TGAAACTTATCCGCCACAGAATGCGATTAGCCTTATCACATGGATGGAAGTGATGGTGGGCGCAAAAAAATATCATCAGG
AAAACCGTACGCGAATTGCGCTGAATGCGTTCAATGTGATTGGCGTTACCCAGGAAATCGCGGAACGAAGCGTCAGCCTC
AGGCAGGTGTACGGAATGAAACTGCCGGACGCTATTATCCTTGCAACAGCGCAGATTCATCGTTGTGAACTTGTGACGCG
CAATACGAAAGACTTTGCCGGGCTGCCGGGCGTAATCATACCCTATAACTTATAG

Antitoxin

Protein

• Length: 81 a.a.
• Molecular weight: 9308.55 Da
• Isoelectric Point: 4.4189

>AT24512 WP_162467731.1 NC_013716:c4076364-4076122 [Citrobacter rodentium ICC168]
MMAGRDMGRILLDLSDDVLQRLDDLKKQRNLSRAELLREAIEQYLAKQGLAENTISNALGLWQGCEEDGVEYERKLREEW

Nucleotide

• Length: 243 bp

>AT24512 NC_013716:c4076364-4076122 [Citrobacter rodentium ICC168]
ATGATGGCTGGAAGAGATATGGGCAGGATATTACTCGACTTATCAGATGACGTGCTCCAGCGTCTTGATGACCTGAAAAA
ACAGCGCAATCTTTCGCGTGCAGAGTTGCTACGCGAAGCGATTGAACAATATCTTGCAAAGCAGGGTTTGGCTGAAAATA
CCATTTCCAATGCGCTGGGTCTTTGGCAGGGTTGTGAGGAAGATGGCGTGGAATACGAACGGAAACTGCGCGAGGAGTGG
TGA

Structures

Toxin

• AlphaFold DB: D2TUA6