Detailed information of TA system TA162056

Bioinformatically predicted

Overview

TA module

• Type: II
• Classification (family/domain): vapBC/VapC-Phd
• Location: 7282420..7283126
• Replicon: chromosome
• Accession: NZ_CP055233
• Organism: Bradyrhizobium diazoefficiens strain 113-2

Toxin (Protein)

• Gene name: vapC
• Uniprot ID: Q89SG6
• Locus tag: HUW42_RS34400
• Protein ID: WP_011085221.1
• Coordinates: 7282701..7283126 (+)
• Length: 142 a.a.

Antitoxin (Protein)

• Gene name: vapB
• Uniprot ID: Q89SG5
• Locus tag: HUW42_RS34395
• Protein ID: WP_011085222.1
• Coordinates: 7282420..7282704 (+)
• Length: 95 a.a.

Genomic Context

Locus tag	Coordinates	Strand	Size (bp)	Protein ID	Product	Description
HUW42_RS34375	7277492..7278466	-	975	WP_011085226.1	sugar ABC transporter permease	-
HUW42_RS34380	7278466..7279551	-	1086	WP_011085225.1	ABC transporter ATP-binding protein	-
HUW42_RS34385	7279564..7280640	-	1077	WP_011085224.1	ABC transporter ATP-binding protein	-
HUW42_RS34390	7280637..7282187	-	1551	WP_011085223.1	glycerol-3-phosphate dehydrogenase	-
HUW42_RS34395	7282420..7282704	+	285	WP_011085222.1	type II toxin-antitoxin system Phd/YefM family antitoxin	Antitoxin
HUW42_RS34400	7282701..7283126	+	426	WP_011085221.1	type II toxin-antitoxin system VapC family toxin	Toxin
HUW42_RS34405	7283129..7283974	-	846	WP_011085220.1	DeoR/GlpR family DNA-binding transcription regulator	-
HUW42_RS34410	7284066..7284752	-	687	WP_038967389.1	HAD-IA family hydrolase	-
HUW42_RS34415	7284908..7285375	+	468	WP_011085218.1	nuclear transport factor 2 family protein	-
HUW42_RS34420	7285477..7285668	-	192	WP_028175062.1	hypothetical protein	-
HUW42_RS34425	7285860..7286291	-	432	WP_178372790.1	acyl-CoA thioesterase	-
HUW42_RS34430	7286371..7287123	-	753	WP_162494065.1	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: 15448.66 Da
• Isoelectric Point: 5.5776

>T162056 WP_011085221.1 NZ_CP055233:7282701-7283126 [Bradyrhizobium diazoefficiens]
VNLLLDTNVLSEVQRPAPSPKVLAWLDTIDEDRAFISVASIAELRRGIALLEDGRRRSALAAWLAHDLPARFADRVLPID
HAVAEHWGDLMAQSRRSGVTLSVMDGFFAATALAHSLSLVTRNVKDFAAFGVPLLNPWDDP

Nucleotide

• Length: 426 bp

>T162056 NZ_CP071512:958304-958453 [Staphylococcus haemolyticus]
ATGACTAAAAATAAAGATTCAGAATTAAATTATCATGAGGAAGAAAATGCGATGGTTCAAGATTTAGATGACTTGAAAAC
ATTGGGCAAAGAAATGGAACAAATTTCTGAAGAAAACGACGAGGACAGGTTGAATCAATCGCATGAGTAA

Antitoxin

Protein

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

>AT162056 WP_011085222.1 NZ_CP055233:7282420-7282704 [Bradyrhizobium diazoefficiens]
MADHNTAPDTLPADDTWTLANAKARLSQVIDRAQTGPQIITRHGKPNAVIVSAEEWARKTARKGTLAEFLLASPLRGADL
ALERMHDAPRDEMP

Nucleotide

• Length: 285 bp

>AT162056 NZ_CP071512:957682-958281 [Staphylococcus haemolyticus]
ATGGCAATGAACTTTAAAGTATTTAATGATGTAGAACATGTAGCTGAGTACACAGCAGATATCATTAGAAAGCAATTTAA
TAACAACCCTACAACTATTGCGGGAATTCATTTAACAAAGGATGCTGCACCTGTTTTAGATGAGTTAAAGAAAGATGTAG
ATCATAATGCGGTTGATTTTAGTCAAGTAAATATCTTAGATTATGACGATAATCGCTCATACTATGAAGCATTAGGTGTA
CCTACTAGTCAAATTTATCCGATTAATCTTGACGATGATGCAGAATCTTTAATTGATGACAAAATTAAAACTAAAGAAAA
TAAAGGTAAATTAATTTTACAAGTTACTTCTATTGATGAATCAGGTAGTTTAAATGTAAATGTAAGACAAGGATTATTAA
AAGCGCGTGAAGTAGTATTAGTTGTGACTGGTGCTAATAAACGTGAAGTTGTTAAAAAACTTTATGAAGAAAATGGTAAA
TCTAGCTTTGAACCAGCTGATTTAAAAGCTCATAGAATGGTAACAGTTGTTTTAGATAGAGCAGCTGCAGAAGGTTTACC
TGAAGATGTTAAAGAATATTTCACTGCTAGATTTGCTTAA

Structures

Toxin

• AlphaFold DB: Q89SG6

Antitoxin

• AlphaFold DB: Q89SG5