Detailed information of TA system TA105992

Bioinformatically predicted

Overview

TA module

• Type: II
• Classification (family/domain): vapBC/VapC-Phd
• Location: 2872226..2872932
• Replicon: chromosome
• Accession: NZ_CP029603
• Organism: Bradyrhizobium diazoefficiens strain XF7

Toxin (Protein)

• Gene name: vapC
• Uniprot ID: Q89SG6
• Locus tag: DI395_RS13045
• Protein ID: WP_011085221.1
• Coordinates: 2872226..2872651 (-)
• Length: 142 a.a.

Antitoxin (Protein)

• Gene name: vapB
• Uniprot ID: Q89SG5
• Locus tag: DI395_RS13050
• Protein ID: WP_011085222.1
• Coordinates: 2872648..2872932 (-)
• Length: 95 a.a.

Genomic Context

Locus tag	Coordinates	Strand	Size (bp)	Protein ID	Product	Description
DI395_RS13015	2868229..2868981	+	753	WP_162494065.1	fatty acid desaturase family protein	-
DI395_RS13020	2869061..2869492	+	432	WP_011085217.1	acyl-CoA thioesterase	-
DI395_RS13025	2869684..2869875	+	192	WP_028175062.1	hypothetical protein	-
DI395_RS13030	2869977..2870444	-	468	WP_011085218.1	nuclear transport factor 2 family protein	-
DI395_RS13035	2870600..2871286	+	687	WP_038967389.1	HAD-IA family hydrolase	-
DI395_RS13040	2871378..2872223	+	846	WP_011085220.1	DeoR/GlpR family DNA-binding transcription regulator	-
DI395_RS13045	2872226..2872651	-	426	WP_011085221.1	type II toxin-antitoxin system VapC family toxin	Toxin
DI395_RS13050	2872648..2872932	-	285	WP_011085222.1	type II toxin-antitoxin system Phd/YefM family antitoxin	Antitoxin
DI395_RS13055	2873165..2874715	+	1551	WP_011085223.1	glycerol-3-phosphate dehydrogenase	-
DI395_RS13060	2874712..2875788	+	1077	WP_011085224.1	ABC transporter ATP-binding protein	-
DI395_RS13065	2875801..2876886	+	1086	WP_011085225.1	ABC transporter ATP-binding protein	-
DI395_RS13070	2876886..2877860	+	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

>T105992 WP_011085221.1 NZ_CP029603:c2872651-2872226 [Bradyrhizobium diazoefficiens]
VNLLLDTNVLSEVQRPAPSPKVLAWLDTIDEDRAFISVASIAELRRGIALLEDGRRRSALAAWLAHDLPARFADRVLPID
HAVAEHWGDLMAQSRRSGVTLSVMDGFFAATALAHSLSLVTRNVKDFAAFGVPLLNPWDDP

Nucleotide

• Length: 426 bp

>T105992 NZ_CP029603:c2872651-2872226 [Bradyrhizobium diazoefficiens]
GTGAACCTGCTGCTCGACACCAACGTACTGTCGGAAGTTCAGCGGCCAGCCCCCTCGCCGAAAGTCTTGGCTTGGCTTGA
CACGATCGATGAAGATCGTGCGTTCATCAGCGTCGCATCGATCGCCGAGCTTCGCCGCGGCATCGCATTGCTGGAGGACG
GCCGCCGGCGCTCGGCACTGGCCGCCTGGCTCGCCCACGATCTACCGGCGCGGTTTGCCGACCGCGTCCTGCCGATCGAC
CACGCGGTGGCCGAGCACTGGGGCGACCTGATGGCTCAGAGCCGCAGGAGCGGCGTCACATTGTCTGTCATGGACGGCTT
CTTTGCCGCAACCGCGCTCGCGCACAGCCTCTCGCTCGTCACGCGCAACGTGAAGGATTTCGCTGCATTCGGCGTCCCCC
TGCTCAATCCGTGGGACGACCCATAG

Antitoxin

Protein

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

>AT105992 WP_011085222.1 NZ_CP029603:c2872932-2872648 [Bradyrhizobium diazoefficiens]
MADHNTAPDTLPADDTWTLANAKARLSQVIDRAQTGPQIITRHGKPNAVIVSAEEWARKTARKGTLAEFLLASPLRGADL
ALERMHDAPRDEMP

Nucleotide

• Length: 285 bp

>AT105992 NZ_CP029603:c2872932-2872648 [Bradyrhizobium diazoefficiens]
ATGGCCGATCACAACACTGCACCCGACACGCTTCCGGCTGATGACACGTGGACGCTTGCCAACGCCAAGGCACGACTGTC
CCAGGTGATCGACCGCGCCCAAACCGGCCCGCAGATCATCACCCGTCACGGCAAGCCGAACGCCGTGATCGTTTCCGCAG
AGGAATGGGCCCGCAAGACCGCACGCAAAGGCACGTTGGCCGAATTCCTACTGGCCTCGCCGCTGCGCGGCGCCGACCTC
GCACTTGAACGCATGCACGATGCGCCGCGCGACGAGATGCCGTGA

Structures

Toxin

• AlphaFold DB: Q89SG6

Antitoxin

• AlphaFold DB: Q89SG5