Detailed information of TA system TA021554

Bioinformatically predicted

Overview

TA module

• Type: II
• Classification (family/domain): vapBC/LOTUS_5_Limkain_b1-Phd
• Location: 232652..233364
• Replicon: plasmid 1
• Accession: NC_007959
• Organism: Nitrobacter hamburgensis X14

Toxin (Protein)

• Gene name: vapC
• Uniprot ID: Q1QFV9
• Locus tag: NHAM_RS21900
• Protein ID: WP_011504851.1
• Coordinates: 232652..233089 (-)
• Length: 146 a.a.

Antitoxin (Protein)

• Gene name: vapB
• Uniprot ID: Q1QFV8
• Locus tag: NHAM_RS21905
• Protein ID: WP_011504850.1
• Coordinates: 233086..233364 (-)
• Length: 93 a.a.

Genomic Context

Locus tag	Coordinates	Strand	Size (bp)	Protein ID	Product	Description
NHAM_RS21880	228625..229641	-	1017	WP_157043838.1	plasmid partitioning protein RepB	-
NHAM_RS21885	229626..230822	-	1197	WP_041359560.1	plasmid partitioning protein RepA	-
NHAM_RS21890	231055..232259	-	1205	Protein_256	site-specific integrase	-
NHAM_RS21895	232283..232655	-	373	Protein_257	hypothetical protein	-
NHAM_RS21900	232652..233089	-	438	WP_011504851.1	type II toxin-antitoxin system VapC family toxin	Toxin
NHAM_RS21905	233086..233364	-	279	WP_011504850.1	type II toxin-antitoxin system Phd/YefM family antitoxin	Antitoxin
NHAM_RS21910	233422..233661	-	240	WP_011504849.1	hypothetical protein	-
NHAM_RS27770	233663..235021	-	1359	WP_198137062.1	TniB family NTP-binding protein	-
NHAM_RS21920	234966..236609	-	1644	WP_011504847.1	Mu transposase C-terminal domain-containing protein	-
NHAM_RS21925	236720..237670	+	951	WP_011504846.1	DUF1612 and helix-turn-helix domain-containing protein	-

Associated MGEs

MGE detail	Similar MGEs	Relative position	MGE Type	Cargo ARG	Virulence gene	Coordinates	Length (bp)
	-	inside	Non-Mobilizable plasmid	-	-	1..294829	294829

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 (3-125)

Antitoxin

• Type II toxin-antitoxin system, antitoxin Phd/YefM (13-59)

Sequences

Toxin

Protein

• Length: 146 a.a.
• Molecular weight: 15853.07 Da
• Isoelectric Point: 4.6326

>T21554 WP_011504851.1 NC_007959:c233089-232652 [Nitrobacter hamburgensis X14]
MNVLLDTKVLSEVRRSAPDPKVLAWLDTIDEDRAFISVASIAELKRGIALMDDGRRREALTAWLAEDLTARFAGRIVPID
PAIAERWGDLMAQARQSGFALSAMDGFFAATAHDRDLVLATRNTKDFAPLGVALFNPWTDEGAPG

Nucleotide

• Length: 438 bp

>T21554 NC_007959:c233089-232652 [Nitrobacter hamburgensis X14]
ATGAATGTCCTGCTCGACACCAAGGTGCTGTCGGAGGTTCGCCGGTCGGCGCCCGACCCGAAGGTGCTCGCCTGGCTCGA
CACGATCGACGAGGACCGCGCCTTCATCAGCGTGGCGTCGATCGCCGAGCTCAAGCGCGGCATTGCGCTGATGGACGATG
GCCGGCGTCGCGAGGCGCTTACCGCCTGGCTTGCGGAGGATCTGACGGCGCGCTTCGCCGGGCGAATTGTGCCAATCGAT
CCCGCGATCGCCGAACGCTGGGGCGATCTGATGGCACAAGCCCGCCAGAGCGGCTTTGCGCTCTCCGCCATGGACGGGTT
TTTCGCAGCCACCGCCCATGACCGTGACCTCGTGCTCGCGACCCGCAACACCAAGGATTTTGCGCCGCTGGGCGTGGCGC
TGTTCAACCCCTGGACCGACGAAGGAGCGCCGGGATGA

Antitoxin

Protein

• Length: 93 a.a.
• Molecular weight: 10261.59 Da
• Isoelectric Point: 6.4699

>AT21554 WP_011504850.1 NC_007959:c233364-233086 [Nitrobacter hamburgensis X14]
VTASRNTPAPDSDHWTVAGAKARLSEVIERAQSDPQIITRHGKPSVVMVSAEEWARKTVRKGTLAEFLMASPLRDADLDL
ERLRDQPRDLDL

Nucleotide

• Length: 279 bp

>AT21554 NC_007959:c233364-233086 [Nitrobacter hamburgensis X14]
GTGACAGCCTCCCGCAACACCCCAGCGCCCGACTCTGACCATTGGACGGTGGCCGGCGCCAAGGCGCGCCTCTCCGAGGT
GATCGAGCGCGCCCAGAGCGACCCGCAGATCATTACCCGCCACGGCAAGCCGAGCGTCGTCATGGTCTCGGCCGAGGAAT
GGGCGCGCAAGACGGTCCGCAAGGGCACGCTGGCCGAGTTCCTGATGGCGTCGCCGCTGCGTGACGCCGATCTGGATCTC
GAGCGGCTCCGCGATCAGCCGCGCGACCTTGATCTATGA

Structures

Toxin

• AlphaFold DB: Q1QFV9

Antitoxin

• AlphaFold DB: Q1QFV8