Detailed information of TA system TA030871

Bioinformatically predicted

Overview

TA module

• Type: II
• Classification (family/domain): vapBC/LOTUS_5_Limkain_b1-Phd
• Location: 6164829..6165535
• Replicon: plasmid pLOOC260-2
• Accession: NZ_AP014685
• Organism: Bradyrhizobium diazoefficiens strain NK6

Toxin (Protein)

• Gene name: vapC
• Uniprot ID: A0A0E4FZY5
• Locus tag: NK6_RS29585
• Protein ID: WP_060910814.1
• Coordinates: 6164829..6165254 (-)
• Length: 142 a.a.

Antitoxin (Protein)

• Gene name: vapB
• Uniprot ID: A0A0E4BT03
• Locus tag: NK6_RS29590
• Protein ID: WP_060910815.1
• Coordinates: 6165251..6165535 (-)
• Length: 95 a.a.

Genomic Context

Locus tag	Coordinates	Strand	Size (bp)	Protein ID	Product	Description
NK6_RS29555	6160776..6161586	+	811	Protein_5811	Kua-ubiquitin conjugating enzyme hybrid localization domain containing protein	-
NK6_RS29560	6161666..6162097	+	432	WP_028175063.1	acyl-CoA thioesterase	-
NK6_RS29565	6162289..6162480	+	192	WP_060910811.1	hypothetical protein	-
NK6_RS29570	6162580..6163047	-	468	WP_060910812.1	nuclear transport factor 2 family protein	-
NK6_RS29575	6163203..6163889	+	687	WP_038967389.1	HAD-IA family hydrolase	-
NK6_RS29580	6163981..6164826	+	846	WP_060910813.1	DeoR/GlpR family DNA-binding transcription regulator	-
NK6_RS29585	6164829..6165254	-	426	WP_060910814.1	type II toxin-antitoxin system VapC family toxin	Toxin
NK6_RS29590	6165251..6165535	-	285	WP_060910815.1	type II toxin-antitoxin system Phd/YefM family antitoxin	Antitoxin
NK6_RS29595	6165769..6167319	+	1551	WP_060910816.1	glycerol-3-phosphate dehydrogenase	-
NK6_RS29600	6167316..6168392	+	1077	WP_060910817.1	ABC transporter ATP-binding protein	-
NK6_RS29605	6168405..6169490	+	1086	WP_060910818.1	ABC transporter ATP-binding protein	-
NK6_RS29610	6169490..6170464	+	975	WP_060910819.1	sugar ABC transporter permease	-

Associated MGEs

MGE detail	Similar MGEs	Relative position	MGE Type	Cargo ARG	Virulence gene	Coordinates	Length (bp)
	-	inside	Non-Mobilizable plasmid	-	tufA / gmd / gmd / kdsB / htpB / acpXL / adeG / adeG / acpXL / kdsA	1..9780023	9780023

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: 15447.60 Da
• Isoelectric Point: 4.3475

>T30871 WP_060910814.1 NZ_AP014685:c6165254-6164829 [Bradyrhizobium diazoefficiens]
VNLLLDTNVLSEVQRPAPSPNVLAWLDTIDEDRAFISVASIAELCRGIALLEDGRRRSALAAWLADDLPTRFGERVLPID
QAVVERWGDLMAQSRRSGVALSVMDGFFAATALANDLTLATRNVKDFAAFGVPLLNPWDDR

Nucleotide

• Length: 426 bp

>T30871 NZ_AP014685:c6165254-6164829 [Bradyrhizobium diazoefficiens]
GTGAACCTGCTGCTCGACACCAACGTACTGTCGGAAGTTCAGCGGCCAGCCCCCTCGCCGAATGTCTTGGCTTGGCTTGA
CACGATCGATGAAGATCGTGCGTTCATCAGCGTCGCATCGATCGCCGAGCTTTGCCGCGGCATCGCATTGCTGGAGGATG
GCCGCCGGCGCTCGGCACTGGCCGCTTGGCTTGCCGATGATCTGCCGACGCGGTTTGGCGAACGTGTCCTGCCGATCGAC
CAGGCGGTGGTCGAGCGCTGGGGCGACCTGATGGCTCAGAGCCGCCGCAGCGGCGTTGCTCTGTCCGTCATGGATGGCTT
CTTTGCCGCGACCGCGCTTGCAAACGATCTCACGCTCGCCACGCGCAATGTGAAGGATTTTGCTGCATTCGGCGTCCCCC
TGCTCAATCCGTGGGACGACCGATAG

Antitoxin

Protein

• Length: 95 a.a.
• Molecular weight: 10224.58 Da
• Isoelectric Point: 6.7256

>AT30871 WP_060910815.1 NZ_AP014685:c6165535-6165251 [Bradyrhizobium diazoefficiens]
MADHNTAPDTLPADDTWTLANAKARLSEVIGRAQTGPQIITRHGKPNAVIVSAEEWARKTARKGTLAEFLLASPLRGADL
ALERMHDAPRDEMP

Nucleotide

• Length: 285 bp

>AT30871 NZ_AP014685:c6165535-6165251 [Bradyrhizobium diazoefficiens]
ATGGCCGATCACAACACTGCACCCGACACGCTTCCGGCTGATGACACGTGGACGCTTGCCAACGCCAAGGCACGACTGTC
CGAGGTGATCGGCCGCGCCCAAACCGGCCCGCAGATCATCACCCGTCACGGCAAGCCGAACGCCGTGATCGTTTCCGCAG
AGGAATGGGCCCGCAAGACCGCACGCAAAGGCACGTTGGCCGAATTCCTGCTGGCCTCGCCGCTGCGCGGCGCCGACCTC
GCACTTGAACGCATGCACGATGCGCCGCGCGACGAGATGCCGTGA

Structures

Toxin

• AlphaFold DB: A0A0E4FZY5

Antitoxin

• AlphaFold DB: A0A0E4BT03