Detailed information of TA system TA088228

Bioinformatically predicted

Overview

TA module

• Type: II
• Classification (family/domain): vapBC/LOTUS_5_Limkain_b1(toxin)
• Location: 4342855..4343471
• Replicon: chromosome
• Accession: NZ_CP024672
• Organism: Citrobacter freundii strain HM38

Toxin (Protein)

• Gene name: vapC
• Uniprot ID: A0A0J1MQ96
• Locus tag: CUC52_RS21415
• Protein ID: WP_003028682.1
• Coordinates: 4343097..4343471 (+)
• Length: 125 a.a.

Antitoxin (Protein)

• Gene name: vapB
• Uniprot ID: -
• Locus tag: CUC52_RS21410
• Protein ID: WP_161958353.1
• Coordinates: 4342855..4343097 (+)
• Length: 81 a.a.

Genomic Context

Locus tag	Coordinates	Strand	Size (bp)	Protein ID	Product	Description
CUC52_RS21380	4338706..4339305	+	600	WP_016151258.1	glucose-1-phosphatase	-
CUC52_RS21385	4339299..4340171	+	873	WP_060854619.1	virulence factor BrkB family protein	-
CUC52_RS21390	4340168..4340605	+	438	WP_003028671.1	D-tyrosyl-tRNA(Tyr) deacylase	-
CUC52_RS21395	4340650..4341591	+	942	WP_003825286.1	fatty acid biosynthesis protein FabY	-
CUC52_RS21405	4341742..4342650	-	909	WP_060854620.1	alpha/beta hydrolase	-
CUC52_RS21410	4342855..4343097	+	243	WP_161958353.1	ribbon-helix-helix domain-containing protein	Antitoxin
CUC52_RS21415	4343097..4343471	+	375	WP_003028682.1	type II toxin-antitoxin system VapC family toxin	Toxin
CUC52_RS21420	4343508..4344437	-	930	WP_003028685.1	formate dehydrogenase accessory protein FdhE	-
CUC52_RS21425	4344434..4345069	-	636	WP_003028686.1	formate dehydrogenase cytochrome b556 subunit	-
CUC52_RS21430	4345066..4345968	-	903	WP_003028691.1	formate dehydrogenase O subunit beta	-

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 (7-112)

Antitoxin

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

Sequences

Toxin

Protein

• Length: 125 a.a.
• Molecular weight: 13674.89 Da
• Isoelectric Point: 9.5622

>T88228 WP_003028682.1 NZ_CP024672:4343097-4343471 [Citrobacter freundii]
MVKGSALFDTNILIDLFSGRNEAKLAIETWPPQNAISLITWMEVMVGAKKYHQEARTRVALGAFNVIGVSQDIAERSVSI
RQEYGMKLPDAIILATAQIHRLTLVTRNTKDFAGLSGVVTPYTL

Nucleotide

• Length: 375 bp

>T88228 NZ_CP024672:4343097-4343471 [Citrobacter freundii]
ATGGTCAAAGGATCCGCGCTTTTTGATACCAACATCCTCATCGATCTGTTTAGTGGGAGAAATGAAGCAAAACTAGCGAT
AGAAACATGGCCGCCGCAGAATGCAATCAGCCTCATTACATGGATGGAGGTGATGGTGGGTGCAAAAAAATACCATCAGG
AAGCCCGTACTCGTGTTGCGCTAGGTGCTTTTAACGTGATCGGCGTTTCACAGGATATTGCTGAACGAAGCGTGAGTATC
AGACAGGAATATGGGATGAAATTGCCGGATGCCATTATTTTGGCAACAGCACAGATTCATCGTCTTACGCTGGTTACGCG
AAATACTAAGGATTTTGCAGGCCTATCCGGTGTGGTCACACCGTATACATTATAA

Antitoxin

Protein

• Length: 81 a.a.
• Molecular weight: 9481.78 Da
• Isoelectric Point: 4.3437

>AT88228 WP_161958353.1 NZ_CP024672:4342855-4343097 [Citrobacter freundii]
MMTGMDMGRILLDLSDEVIKRLDDLKVQRNLPRAELLREAVEQYLERQDQAETTISRALGLWQGCEEDGVEYQRKLREEW

Nucleotide

• Length: 243 bp

>AT88228 NZ_CP024672:4342855-4343097 [Citrobacter freundii]
ATGATGACTGGGATGGATATGGGCAGAATTTTACTCGATTTATCAGATGAAGTGATTAAACGTCTTGATGATCTCAAGGT
GCAGCGCAACCTGCCGCGAGCAGAACTTTTACGGGAGGCCGTTGAACAGTATCTTGAGAGGCAGGATCAGGCTGAAACCA
CAATTTCACGTGCTCTTGGGCTGTGGCAAGGCTGTGAGGAAGATGGTGTTGAATACCAGCGTAAACTCCGTGAGGAATGG
TAA

Structures

Toxin

• AlphaFold DB: A0A0J1MQ96