Detailed information of TA system TA089454

Bioinformatically predicted

Overview

TA module

• Type: II
• Classification (family/domain): vagCD/VapC-VagC
• Location: 648953..649596
• Replicon: chromosome
• Accession: NZ_CP025003
• Organism: Dickeya fangzhongdai strain DSM 101947

Toxin (Protein)

• Gene name: vagD
• Uniprot ID: -
• Locus tag: CVE23_RS03090
• Protein ID: WP_100848871.1
• Coordinates: 649180..649596 (+)
• Length: 139 a.a.

Antitoxin (Protein)

• Gene name: vagC
• Uniprot ID: A0A2K8QHR2
• Locus tag: CVE23_RS03085
• Protein ID: WP_024109781.1
• Coordinates: 648953..649183 (+)
• Length: 77 a.a.

Genomic Context

Locus tag	Coordinates	Strand	Size (bp)	Protein ID	Product	Description
CVE23_RS03065	644900..646321	+	1422	WP_100850398.1	integrating conjugative element protein	-
CVE23_RS03070	646333..646710	+	378	WP_100848869.1	hypothetical protein	-
CVE23_RS03075	646707..648251	+	1545	WP_024109779.1	conjugal transfer protein TraG N-terminal domain-containing protein	-
CVE23_RS03080	648288..648752	-	465	WP_100848870.1	hypothetical protein	-
CVE23_RS03085	648953..649183	+	231	WP_024109781.1	AbrB/MazE/SpoVT family DNA-binding domain-containing protein	Antitoxin
CVE23_RS03090	649180..649596	+	417	WP_100848871.1	type II toxin-antitoxin system VapC family toxin	Toxin
CVE23_RS22630	649933..650193	+	261	WP_145958402.1	hypothetical protein	-
CVE23_RS03095	650506..650934	+	429	WP_145958438.1	DUF2726 domain-containing protein	-
CVE23_RS03100	651997..652911	+	915	WP_100848873.1	integrase domain-containing protein	-
CVE23_RS03105	653696..653965	+	270	WP_145958403.1	hypothetical protein	-
CVE23_RS03110	654046..654378	+	333	WP_100848875.1	hypothetical protein	-

Associated MGEs

MGE detail	Similar MGEs	Relative position	MGE Type	Cargo ARG	Virulence gene	Coordinates	Length (bp)
	-	inside	Integrative and Conjugative Element	-	-	595155..675244	80089

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 (7-55)

Sequences

Toxin

Protein

• Length: 139 a.a.
• Molecular weight: 15042.51 Da
• Isoelectric Point: 7.6437

>T89454 WP_100848871.1 NZ_CP025003:649180-649596 [Dickeya fangzhongdai]
MSKTYMLDTCTCSFIMREQPEAVLKRLEQAVLRRHRIVVSAITYAEMRFGAIGKKASPRHALLVDAFCARLDTVLPWDRA
AVDATTDIKVTLAAVGTPIGNNDAAIAGHAIAADAILVTNNVKEFARVPGLNIEDWCC

Nucleotide

• Length: 417 bp

>T89454 NZ_CP025003:649180-649596 [Dickeya fangzhongdai]
ATGAGTAAGACCTACATGCTCGATACCTGTACTTGCTCCTTTATAATGCGTGAACAACCAGAAGCAGTACTGAAGCGACT
TGAGCAAGCCGTACTGAGACGTCACCGTATTGTGGTGTCGGCTATTACTTATGCCGAAATGCGGTTCGGAGCAATTGGAA
AAAAGGCTTCGCCACGCCATGCGTTGCTGGTTGATGCGTTTTGTGCTCGCCTTGATACTGTGCTGCCATGGGATCGTGCC
GCGGTGGATGCCACCACAGACATCAAGGTTACGCTGGCTGCTGTCGGCACACCGATTGGTAACAATGACGCAGCTATTGC
CGGGCATGCTATTGCGGCGGACGCCATTTTGGTGACCAATAATGTGAAGGAGTTTGCACGGGTACCGGGACTAAATATTG
AAGATTGGTGCTGTTGA

Antitoxin

Protein

• Length: 77 a.a.
• Molecular weight: 8824.88 Da
• Isoelectric Point: 4.2917

>AT89454 WP_024109781.1 NZ_CP025003:648953-649183 [Dickeya fangzhongdai]
MRTVSVFKNGNNRAIRLPRDLDFEGVNELEIVREGDTIILRPVKPTWSSFLQEEKADSDFLIEREDVVSDEGRFDL

Nucleotide

• Length: 231 bp

>AT89454 NZ_CP025003:648953-649183 [Dickeya fangzhongdai]
ATGCGAACTGTATCTGTATTTAAAAATGGCAATAACCGTGCCATCCGTCTGCCTCGTGATCTGGACTTTGAGGGTGTTAA
CGAGCTGGAGATAGTCCGTGAAGGTGACACGATTATCCTCCGTCCGGTCAAACCCACCTGGAGTTCGTTCCTGCAGGAAG
AGAAAGCCGATTCAGACTTTCTGATTGAACGTGAAGATGTTGTCAGTGATGAGGGTCGTTTTGATCTATGA

Structures

Antitoxin

• AlphaFold DB: A0A2K8QHR2