Detailed information of TA system TA028402

Bioinformatically predicted

Overview

TA module

• Type: II
• Classification (family/domain): vapBC/VapC-VagC
• Location: 2609359..2609990
• Replicon: chromosome
• Accession: NC_018700
• Organism: Sinorhizobium meliloti Rm41

Toxin (Protein)

• Gene name: vapC
• Uniprot ID: -
• Locus tag: BN406_RS12845
• Protein ID: WP_013844828.1
• Coordinates: 2609359..2609757 (-)
• Length: 133 a.a.

Antitoxin (Protein)

• Gene name: vapB
• Uniprot ID: Q92MD9
• Locus tag: BN406_RS12850
• Protein ID: WP_010970129.1
• Coordinates: 2609757..2609990 (-)
• Length: 78 a.a.

Genomic Context

Locus tag	Coordinates	Strand	Size (bp)	Protein ID	Product	Description
BN406_RS12810	2604441..2604743	-	303	WP_010970122.1	type II toxin-antitoxin system RelE/ParE family toxin	-
BN406_RS12815	2604740..2605015	-	276	WP_010970123.1	type II toxin-antitoxin system ParD family antitoxin	-
BN406_RS34760	2605301..2605450	+	150	WP_010970124.1	hypothetical protein	-
BN406_RS12825	2605447..2606382	+	936	WP_010970125.1	site-specific tyrosine recombinase XerD	-
BN406_RS12830	2606446..2607399	+	954	WP_003527479.1	acetyl-CoA carboxylase carboxyltransferase subunit alpha	-
BN406_RS12835	2607644..2609086	+	1443	WP_015007947.1	murein L,D-transpeptidase	-
BN406_RS12840	2609086..2609325	+	240	WP_010970127.1	sulfurtransferase TusA family protein	-
BN406_RS12845	2609359..2609757	-	399	WP_013844828.1	type II toxin-antitoxin system toxin VapC	Toxin
BN406_RS12850	2609757..2609990	-	234	WP_010970129.1	AbrB/MazE/SpoVT family DNA-binding domain-containing protein	Antitoxin
BN406_RS12855	2610099..2611244	-	1146	WP_010970130.1	GTP-binding protein	-
BN406_RS12860	2611258..2612340	-	1083	WP_010970131.1	D-alanyl-D-alanine carboxypeptidase	-
BN406_RS12865	2612592..2613755	+	1164	WP_010970132.1	amidohydrolase	-
BN406_RS12870	2613778..2614242	+	465	WP_010970133.1	Lrp/AsnC ligand binding domain-containing 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

• SpoVT-AbrB domain (7-56)

Sequences

Toxin

Protein

• Length: 133 a.a.
• Molecular weight: 14829.13 Da
• Isoelectric Point: 6.9581

>T28402 WP_013844828.1 NC_018700:c2609757-2609359 [Sinorhizobium meliloti Rm41]
MLTYMLDTNICIYVMKTYPPAVREKFNGLAEQLCISSITLGELHYGAEKSARRVENLTAIEHFVARLEVLPFADKAAAHY
GQVRAELERTGTPCGPHDMQIGAHARSEGLIVVTNNIREFVRMPGVRVENWL

Nucleotide

• Length: 399 bp

>T28402 NC_018700:c2609757-2609359 [Sinorhizobium meliloti Rm41]
ATGCTCACCTATATGCTCGATACCAATATCTGCATCTATGTGATGAAGACCTATCCGCCGGCCGTGCGCGAAAAGTTCAA
CGGACTGGCGGAGCAGCTTTGCATATCGAGCATCACGCTGGGAGAATTACACTATGGCGCCGAAAAATCGGCCCGGCGCG
TTGAGAACCTTACGGCTATCGAACATTTCGTGGCACGGCTGGAGGTGCTGCCGTTCGCAGACAAGGCAGCGGCCCACTAC
GGGCAGGTTCGGGCTGAACTGGAGCGGACGGGAACGCCATGCGGCCCTCATGACATGCAGATCGGCGCGCATGCGCGCAG
CGAAGGGCTGATTGTCGTGACCAACAATATACGCGAGTTCGTCCGCATGCCGGGTGTAAGGGTCGAGAACTGGCTGTGA

Antitoxin

Protein

• Length: 78 a.a.
• Molecular weight: 8673.87 Da
• Isoelectric Point: 8.9167

>AT28402 WP_010970129.1 NC_018700:c2609990-2609757 [Sinorhizobium meliloti Rm41]
MASSTVFISNRSQAVRLPKAVAFPEGVHQVDILKIGRSRVIVPQGKRWDDLFLSGPRVSEDFMSERDQPVAETRESF

Nucleotide

• Length: 234 bp

>AT28402 NC_018700:c2609990-2609757 [Sinorhizobium meliloti Rm41]
TTGGCCAGTTCGACCGTATTCATCAGTAACCGTAGCCAGGCGGTGCGGCTGCCAAAGGCCGTCGCCTTTCCCGAGGGCGT
GCATCAGGTCGATATCCTCAAGATCGGCCGCAGCCGCGTGATCGTCCCCCAGGGCAAAAGATGGGACGATCTGTTCCTCA
GCGGGCCGCGCGTCAGCGAGGATTTCATGAGCGAGCGTGATCAGCCGGTGGCGGAAACACGCGAATCCTTCTGA

Structures

Antitoxin

• AlphaFold DB: Q92MD9