Detailed information of TA system TA112000

Bioinformatically predicted

Overview

TA module

• Type: II
• Classification (family/domain): vapBC/VapC-Phd
• Location: 2587945..2588651
• Replicon: chromosome
• Accession: NZ_CP032617
• Organism: Bradyrhizobium diazoefficiens strain 110spc4

Toxin (Protein)

• Gene name: vapC
• Uniprot ID: Q89SG6
• Locus tag: Bdiaspc4_RS12445
• Protein ID: WP_011085221.1
• Coordinates: 2587945..2588370 (-)
• Length: 142 a.a.

Antitoxin (Protein)

• Gene name: vapB
• Uniprot ID: Q89SG5
• Locus tag: Bdiaspc4_RS12450
• Protein ID: WP_011085222.1
• Coordinates: 2588367..2588651 (-)
• Length: 95 a.a.

Genomic Context

Locus tag	Coordinates	Strand	Size (bp)	Protein ID	Product	Description
Bdiaspc4_RS12415	2583948..2584700	+	753	WP_162494065.1	fatty acid desaturase family protein	-
Bdiaspc4_RS12420	2584780..2585211	+	432	WP_011085217.1	acyl-CoA thioesterase	-
Bdiaspc4_RS12425	2585403..2585594	+	192	WP_028175062.1	hypothetical protein	-
Bdiaspc4_RS12430	2585696..2586163	-	468	WP_011085218.1	nuclear transport factor 2 family protein	-
Bdiaspc4_RS12435	2586319..2587005	+	687	WP_038967389.1	HAD-IA family hydrolase	-
Bdiaspc4_RS12440	2587097..2587942	+	846	WP_011085220.1	DeoR/GlpR family DNA-binding transcription regulator	-
Bdiaspc4_RS12445	2587945..2588370	-	426	WP_011085221.1	type II toxin-antitoxin system VapC family toxin	Toxin
Bdiaspc4_RS12450	2588367..2588651	-	285	WP_011085222.1	type II toxin-antitoxin system Phd/YefM family antitoxin	Antitoxin
Bdiaspc4_RS12455	2588884..2590434	+	1551	WP_011085223.1	glycerol-3-phosphate dehydrogenase	-
Bdiaspc4_RS12460	2590431..2591507	+	1077	WP_011085224.1	ABC transporter ATP-binding protein	-
Bdiaspc4_RS12465	2591520..2592605	+	1086	WP_011085225.1	ABC transporter ATP-binding protein	-
Bdiaspc4_RS12470	2592605..2593579	+	975	WP_011085226.1	sugar ABC transporter permease	-

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 (4-123)

Antitoxin

• Type II toxin-antitoxin system, antitoxin Phd/YefM (15-77)

Sequences

Toxin

Protein

• Length: 142 a.a.
• Molecular weight: 15448.66 Da
• Isoelectric Point: 5.5776

>T112000 WP_011085221.1 NZ_CP032617:c2588370-2587945 [Bradyrhizobium diazoefficiens]
VNLLLDTNVLSEVQRPAPSPKVLAWLDTIDEDRAFISVASIAELRRGIALLEDGRRRSALAAWLAHDLPARFADRVLPID
HAVAEHWGDLMAQSRRSGVTLSVMDGFFAATALAHSLSLVTRNVKDFAAFGVPLLNPWDDP

Nucleotide

• Length: 426 bp

>T112000 NZ_CP032617:c2588370-2587945 [Bradyrhizobium diazoefficiens]
GTGAACCTGCTGCTCGACACCAACGTACTGTCGGAAGTTCAGCGGCCAGCCCCCTCGCCGAAAGTCTTGGCTTGGCTTGA
CACGATCGATGAAGATCGTGCGTTCATCAGCGTCGCATCGATCGCCGAGCTTCGCCGCGGCATCGCATTGCTGGAGGACG
GCCGCCGGCGCTCGGCACTGGCCGCCTGGCTCGCCCACGATCTACCGGCGCGGTTTGCCGACCGCGTCCTGCCGATCGAC
CACGCGGTGGCCGAGCACTGGGGCGACCTGATGGCTCAGAGCCGCAGGAGCGGCGTCACATTGTCTGTCATGGACGGCTT
CTTTGCCGCAACCGCGCTCGCGCACAGCCTCTCGCTCGTCACGCGCAACGTGAAGGATTTCGCTGCATTCGGCGTCCCCC
TGCTCAATCCGTGGGACGACCCATAG

Antitoxin

Protein

• Length: 95 a.a.
• Molecular weight: 10281.64 Da
• Isoelectric Point: 6.7251

>AT112000 WP_011085222.1 NZ_CP032617:c2588651-2588367 [Bradyrhizobium diazoefficiens]
MADHNTAPDTLPADDTWTLANAKARLSQVIDRAQTGPQIITRHGKPNAVIVSAEEWARKTARKGTLAEFLLASPLRGADL
ALERMHDAPRDEMP

Nucleotide

• Length: 285 bp

>AT112000 NZ_CP032617:c2588651-2588367 [Bradyrhizobium diazoefficiens]
ATGGCCGATCACAACACTGCACCCGACACGCTTCCGGCTGATGACACGTGGACGCTTGCCAACGCCAAGGCACGACTGTC
CCAGGTGATCGACCGCGCCCAAACCGGCCCGCAGATCATCACCCGTCACGGCAAGCCGAACGCCGTGATCGTTTCCGCAG
AGGAATGGGCCCGCAAGACCGCACGCAAAGGCACGTTGGCCGAATTCCTACTGGCCTCGCCGCTGCGCGGCGCCGACCTC
GCACTTGAACGCATGCACGATGCGCCGCGCGACGAGATGCCGTGA

Structures

Toxin

• AlphaFold DB: Q89SG6

Antitoxin

• AlphaFold DB: Q89SG5