Detailed information of TA system TA057970

Bioinformatically predicted

Overview

TA module

• Type: II
• Classification (family/domain): vapBC/LOTUS_5_Limkain_b1-Phd
• Location: 7563020..7563726
• Replicon: chromosome
• Accession: NZ_CP013127
• Organism: Bradyrhizobium diazoefficiens strain USDA 122

Toxin (Protein)

• Gene name: vapC
• Uniprot ID: A0A837CG53
• Locus tag: BD122_RS35700
• Protein ID: WP_028175059.1
• Coordinates: 7563301..7563726 (+)
• Length: 142 a.a.

Antitoxin (Protein)

• Gene name: vapB
• Uniprot ID: A0A837CFL2
• Locus tag: BD122_RS35695
• Protein ID: WP_028175058.1
• Coordinates: 7563020..7563304 (+)
• Length: 95 a.a.

Genomic Context

Locus tag	Coordinates	Strand	Size (bp)	Protein ID	Product	Description
BD122_RS35675	7558093..7559067	-	975	WP_011085226.1	sugar ABC transporter permease	-
BD122_RS35680	7559067..7560152	-	1086	WP_011085225.1	ABC transporter ATP-binding protein	-
BD122_RS35685	7560165..7561241	-	1077	WP_028175056.1	ABC transporter ATP-binding protein	-
BD122_RS35690	7561238..7562788	-	1551	WP_028175057.1	glycerol-3-phosphate dehydrogenase	-
BD122_RS35695	7563020..7563304	+	285	WP_028175058.1	type II toxin-antitoxin system Phd/YefM family antitoxin	Antitoxin
BD122_RS35700	7563301..7563726	+	426	WP_028175059.1	type II toxin-antitoxin system VapC family toxin	Toxin
BD122_RS35705	7563729..7564574	-	846	WP_028175060.1	DeoR/GlpR family DNA-binding transcription regulator	-
BD122_RS35710	7564666..7565352	-	687	WP_028175061.1	HAD-IA family hydrolase	-
BD122_RS35715	7565508..7565975	+	468	WP_011085218.1	nuclear transport factor 2 family protein	-
BD122_RS35720	7566075..7566266	-	192	WP_028175062.1	hypothetical protein	-
BD122_RS35725	7566458..7566889	-	432	WP_028175063.1	acyl-CoA thioesterase	-
BD122_RS35730	7566969..7567778	-	810	WP_028175064.1	fatty acid desaturase family protein	-

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: 15514.68 Da
• Isoelectric Point: 4.4561

>T57970 WP_028175059.1 NZ_CP013127:7563301-7563726 [Bradyrhizobium diazoefficiens]
VNLLLDTNILSEVQRPAPSPNVLAWLDTIDEDRAFISVASIAELRRGIALLEDGRRRSALAAWLADDLPTRFGERVLPID
QAVVERWGDLMAQSRRSGVALSVMDGFFAATALANDLTLATRNVKDFAAFGVPLLNPWDDR

Nucleotide

• Length: 426 bp

>T57970 NZ_CP013127:7563301-7563726 [Bradyrhizobium diazoefficiens]
GTGAACCTGCTGCTCGACACCAACATACTGTCGGAAGTTCAGCGGCCAGCCCCCTCGCCGAATGTCTTGGCTTGGCTTGA
CACGATCGATGAAGATCGTGCGTTCATCAGCGTCGCATCGATCGCCGAGCTTCGCCGCGGCATCGCATTGCTGGAGGATG
GCCGCCGGCGCTCGGCACTGGCCGCTTGGCTTGCCGATGATCTGCCGACGCGGTTTGGCGAACGTGTCCTGCCGATCGAC
CAGGCGGTGGTCGAGCGCTGGGGCGACCTGATGGCTCAGAGCCGCCGCAGCGGCGTTGCTCTGTCCGTCATGGATGGCTT
CTTTGCCGCGACCGCGCTTGCAAACGATCTCACGCTCGCCACGCGCAATGTGAAGGATTTTGCCGCATTCGGCGTCCCCC
TGCTCAATCCGTGGGACGACCGATAG

Antitoxin

Protein

• Length: 95 a.a.
• Molecular weight: 10223.50 Da
• Isoelectric Point: 6.7247

>AT57970 WP_028175058.1 NZ_CP013127:7563020-7563304 [Bradyrhizobium diazoefficiens]
MADHNTAPDTLPADDTWTLANAKARLSQVIDRAQTGPQIITRHGKPNAVVVSAEEWARKTARKGTLAEFLLASPLRGADL
ALDRTHDAPRDEMP

Nucleotide

• Length: 285 bp

>AT57970 NZ_CP013127:7563020-7563304 [Bradyrhizobium diazoefficiens]
ATGGCCGATCACAACACTGCACCCGACACGCTTCCGGCTGATGACACGTGGACGCTTGCCAACGCCAAGGCACGACTGTC
CCAGGTGATCGACCGCGCCCAAACCGGCCCGCAGATCATCACCCGTCACGGCAAGCCCAATGCGGTGGTCGTTTCCGCCG
AGGAATGGGCCCGCAAGACCGCACGCAAAGGCACGTTGGCCGAATTCCTGCTGGCCTCTCCGCTGCGCGGCGCCGACCTC
GCACTTGATCGCACGCACGATGCGCCGCGCGACGAGATGCCGTGA

Structures

Toxin

• AlphaFold DB: A0A837CG53

Antitoxin

• AlphaFold DB: A0A837CFL2