Detailed information of TA system TA020646

Bioinformatically predicted

Overview

TA module

• Type: II
• Classification (family/domain): vapBC/LOTUS_5_Limkain_b1-RHH
• Location: 1397530..1398104
• Replicon: chromosome
• Accession: NC_003047
• Organism: Sinorhizobium meliloti 1021

Toxin (Protein)

• Gene name: vapC
• Uniprot ID: Q92QN4
• Locus tag: SM_RS06540
• Protein ID: WP_010969154.1
• Coordinates: 1397530..1397895 (-)
• Length: 122 a.a.

Antitoxin (Protein)

• Gene name: vapB
• Uniprot ID: Q92QN3
• Locus tag: SM_RS06545
• Protein ID: WP_010969155.1
• Coordinates: 1397889..1398104 (-)
• Length: 72 a.a.

Genomic Context

Locus tag	Coordinates	Strand	Size (bp)	Protein ID	Product	Description
SM_RS06515 (SMc01927)	1392670..1394112	+	1443	WP_010969150.1	NADH-quinone oxidoreductase subunit NuoN	-
SM_RS06520 (SMc01928)	1394109..1394876	+	768	WP_003531861.1	biotin--[acetyl-CoA-carboxylase] ligase	-
SM_RS06525 (SMc01929)	1394904..1396571	+	1668	WP_010969151.1	ribonuclease J	-
SM_RS06530 (SMc01930)	1396630..1397034	+	405	WP_010969152.1	methylmalonyl-CoA epimerase	-
SM_RS06535 (SMc01931)	1397174..1397443	+	270	WP_014526683.1	DUF1467 family protein	-
SM_RS06540 (SMc01932)	1397530..1397895	-	366	WP_010969154.1	type II toxin-antitoxin system VapC family toxin	Toxin
SM_RS06545 (SMc01933)	1397889..1398104	-	216	WP_010969155.1	ribbon-helix-helix protein, CopG family	Antitoxin
SM_RS06550	1398172..1398399	-	228	WP_017264047.1	hypothetical protein	-
SM_RS06555 (SMc01934)	1398815..1400143	+	1329	WP_003531873.1	proline--tRNA ligase	-
SM_RS06560 (SMc01935)	1400164..1401474	+	1311	WP_014529722.1	lipoprotein-releasing ABC transporter permease subunit	-
SM_RS06565 (SMc01376)	1401492..1402178	+	687	WP_010969157.1	ABC transporter ATP-binding 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 (5-106)

Antitoxin

• Ribbon-helix-helix protein, CopG (9-40)

Sequences

Toxin

Protein

• Length: 122 a.a.
• Molecular weight: 13592.57 Da
• Isoelectric Point: 5.1787

>T20646 WP_010969154.1 NC_003047:c1397895-1397530 [Sinorhizobium meliloti 1021]
MVGALFDTNILIDHLNAVPQAHKELDRFENRAISIITWMEVMVGADAELVEPTRRFLDGFETIALNDEIANRAVTLRRAH
RIKLPDAVIWATAQTAGRLLVTRNTKDFPADDPGIREPYAV

Nucleotide

• Length: 366 bp

>T20646 NC_003047:c1397895-1397530 [Sinorhizobium meliloti 1021]
ATGGTAGGCGCACTGTTCGATACCAATATCCTTATCGATCATCTGAATGCGGTGCCTCAGGCGCACAAGGAACTTGACCG
TTTCGAAAACCGGGCCATCAGCATCATCACCTGGATGGAGGTGATGGTTGGAGCGGACGCCGAACTGGTTGAGCCGACCC
GGCGCTTCCTCGACGGTTTCGAAACGATCGCCTTGAACGATGAGATCGCCAACCGTGCGGTGACATTGCGCAGGGCGCAC
CGCATCAAGCTACCCGACGCGGTGATCTGGGCAACGGCGCAGACTGCCGGTCGTCTGCTCGTGACGCGCAATACCAAGGA
CTTTCCAGCCGACGACCCGGGGATACGCGAACCCTACGCCGTGTAG

Antitoxin

Protein

• Length: 72 a.a.
• Molecular weight: 8381.51 Da
• Isoelectric Point: 8.6052

>AT20646 WP_010969155.1 NC_003047:c1398104-1397889 [Sinorhizobium meliloti 1021]
MRALIDMNDTQVEALDTLAKRVRRSRAALIREAIDDYLNRHHREQIEDGFGLWGKRKVDGLAYQEKVRGEW

Nucleotide

• Length: 216 bp

>AT20646 NC_003047:c1398104-1397889 [Sinorhizobium meliloti 1021]
ATGCGAGCCTTGATCGATATGAACGATACCCAGGTCGAAGCCCTAGATACCCTCGCCAAGCGGGTGCGCCGGTCCCGTGC
GGCTCTGATCCGCGAAGCGATCGACGACTATCTCAACCGTCATCATCGCGAGCAGATCGAAGATGGCTTCGGTTTGTGGG
GCAAGCGCAAAGTTGACGGTCTGGCTTATCAGGAGAAGGTGCGCGGCGAATGGTAG

Structures

Toxin

• AlphaFold DB: Q92QN4

Antitoxin

• AlphaFold DB: Q92QN3