Detailed information of TA system TA029888

Bioinformatically predicted

Overview

TA module

• Type: II
• Classification (family/domain): vapC-vagC/VapC-VagC
• Location: 835095..835732
• Replicon: plasmid pRetMIM1f
• Accession: NC_021911
• Organism: Rhizobium etli bv. mimosae str. Mim1

Toxin (Protein)

• Gene name: vapC
• Uniprot ID: S5S8S3
• Locus tag: REMIM1_RS33290
• Protein ID: WP_020919781.1
• Coordinates: 835331..835732 (+)
• Length: 134 a.a.

Antitoxin (Protein)

• Gene name: vagC
• Uniprot ID: S5SX58
• Locus tag: REMIM1_RS33285
• Protein ID: WP_020919780.1
• Coordinates: 835095..835331 (+)
• Length: 79 a.a.

Genomic Context

Locus tag	Coordinates	Strand	Size (bp)	Protein ID	Product	Description
REMIM1_RS33270	830932..832107	+	1176	WP_020919777.1	type IV secretion system protein VirB10	-
REMIM1_RS33275	832116..833147	+	1032	WP_020919778.1	P-type DNA transfer ATPase VirB11	-
REMIM1_RS33280	833300..834508	-	1209	WP_041679331.1	DUF1173 domain-containing protein	-
REMIM1_RS33285	835095..835331	+	237	WP_020919780.1	AbrB/MazE/SpoVT family DNA-binding domain-containing protein	Antitoxin
REMIM1_RS33290	835331..835732	+	402	WP_020919781.1	type II toxin-antitoxin system VapC family toxin	Toxin
REMIM1_RS33295	835867..836199	-	333	WP_020919782.1	WGR domain-containing protein	-
REMIM1_RS33300	836662..836985	+	324	WP_008530485.1	DUF736 family protein	-
REMIM1_RS37335	837300..837467	+	168	WP_196232147.1	hypothetical protein	-
REMIM1_RS33310	837801..838271	+	471	WP_020919784.1	hypothetical protein	-
REMIM1_RS33315	838449..838718	+	270	WP_020919785.1	type II toxin-antitoxin system prevent-host-death family antitoxin	-
REMIM1_RS33320	838715..839128	+	414	WP_020919786.1	hypothetical protein	-

Associated MGEs

MGE detail	Similar MGEs	Relative position	MGE Type	Cargo ARG	Virulence gene	Coordinates	Length (bp)
	-	inside	Conjugative plasmid	-	htpB	1..1082659	1082659

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 (4-120)

Antitoxin

• SpoVT-AbrB domain (7-46)

Sequences

Toxin

Protein

• Length: 134 a.a.
• Molecular weight: 14912.15 Da
• Isoelectric Point: 4.9309

>T29888 WP_020919781.1 NC_021911:835331-835732 [Rhizobium etli bv. mimosae str. Mim1]
MPLYMLDTNMCIYLMKEQPPQVARRFAECRVGDVVMSAITFAELEYGVSATANAEKERANLEFLIEAIPVAPFDANAARA
YGSVRFATRERKKDHLDKLIAAHALSIDAVLVTNNTRDFSVYEGLPIENWLLS

Nucleotide

• Length: 402 bp

>T29888 NC_021911:835331-835732 [Rhizobium etli bv. mimosae str. Mim1]
ATGCCGCTTTATATGCTCGACACGAACATGTGTATCTACCTGATGAAGGAGCAGCCGCCGCAAGTCGCGCGCCGCTTTGC
TGAATGCCGCGTCGGTGACGTTGTTATGTCAGCCATTACATTTGCTGAACTTGAATATGGTGTCTCTGCCACGGCGAACG
CGGAAAAGGAGCGGGCAAACCTGGAATTCCTGATAGAGGCGATTCCAGTTGCGCCCTTCGACGCCAATGCGGCGCGGGCC
TACGGGTCCGTCAGATTTGCCACGCGCGAACGGAAAAAAGACCATCTGGACAAATTGATAGCCGCTCATGCGCTCTCGAT
TGATGCGGTCCTCGTGACCAACAATACGCGGGACTTTTCTGTCTATGAAGGGTTGCCGATTGAGAACTGGTTGTTGTCGT
GA

Antitoxin

Protein

• Length: 79 a.a.
• Molecular weight: 8907.01 Da
• Isoelectric Point: 5.8451

>AT29888 WP_020919780.1 NC_021911:835095-835331 [Rhizobium etli bv. mimosae str. Mim1]
VHTTKVFKNGNSQAVRIPADLAYSQTEMDLEIERIGDEIRIRPLKPSLEGVLSRFARFDRSFMAEGRGNQEQTERDAL

Nucleotide

• Length: 237 bp

>AT29888 NC_021911:835095-835331 [Rhizobium etli bv. mimosae str. Mim1]
GTGCACACGACCAAGGTATTCAAAAACGGCAACTCACAAGCTGTGCGCATCCCTGCGGATTTGGCTTACAGCCAGACCGA
GATGGACCTTGAAATCGAGCGAATCGGTGACGAGATTCGCATACGCCCGCTGAAGCCGTCCCTGGAAGGCGTGCTTTCGC
GTTTCGCAAGGTTTGACCGCTCGTTCATGGCAGAAGGACGCGGTAATCAGGAGCAGACCGAGCGGGATGCGCTTTAA

Structures

Toxin

• AlphaFold DB: S5S8S3

Antitoxin

• AlphaFold DB: S5SX58