Detailed information of TA system TA029890

Bioinformatically predicted

Overview

TA module

• Type: II
• Classification (family/domain): vapBC/LOTUS_5_Limkain_b1(toxin)
• Location: 1062222..1062796
• Replicon: plasmid pRetMIM1f
• Accession: NC_021911
• Organism: Rhizobium etli bv. mimosae str. Mim1

Toxin (Protein)

• Gene name: vapC
• Uniprot ID: S5SHE0
• Locus tag: REMIM1_RS34365
• Protein ID: WP_020919987.1
• Coordinates: 1062222..1062587 (-)
• Length: 122 a.a.

Antitoxin (Protein)

• Gene name: vapB
• Uniprot ID: S5SXW7
• Locus tag: REMIM1_RS34370
• Protein ID: WP_011428858.1
• Coordinates: 1062581..1062796 (-)
• Length: 72 a.a.

Genomic Context

Locus tag	Coordinates	Strand	Size (bp)	Protein ID	Product	Description
REMIM1_RS34350	1057506..1058891	+	1386	WP_020919984.1	DegQ family serine endoprotease	-
REMIM1_RS34355	1058912..1060735	+	1824	WP_041679422.1	ATP-dependent zinc metalloprotease FtsH	-
REMIM1_RS34360	1061071..1061373	+	303	WP_020919986.1	DUF982 domain-containing protein	-
REMIM1_RS36950	1061370..1061672	-	303	WP_155249502.1	GNAT family N-acetyltransferase	-
REMIM1_RS34365	1062222..1062587	-	366	WP_020919987.1	type II toxin-antitoxin system VapC family toxin	Toxin
REMIM1_RS34370	1062581..1062796	-	216	WP_011428858.1	ribbon-helix-helix domain-containing protein	Antitoxin
REMIM1_RS34375	1063120..1063803	-	684	WP_020919988.1	redoxin domain-containing protein	-
REMIM1_RS34380	1064180..1065226	-	1047	WP_020919989.1	S-adenosylmethionine:tRNA ribosyltransferase-isomerase	-
REMIM1_RS34385	1065223..1065945	-	723	WP_020919990.1	SDR family oxidoreductase	-
REMIM1_RS34390	1066031..1066465	+	435	WP_020919991.1	redox-sensitive transcriptional activator SoxR	-

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 (5-108)

Antitoxin

• Ribbon-helix-helix protein, CopG (5-40)

Sequences

Toxin

Protein

• Length: 122 a.a.
• Molecular weight: 13686.05 Da
• Isoelectric Point: 7.2029

>T29890 WP_020919987.1 NC_021911:c1062587-1062222 [Rhizobium etli bv. mimosae str. Mim1]
MVKSLFDTNVLIDYLNAVPQARDELRRYPEKAISIITWMEVLVGAKPEVAIGTRAFLAGFAVIAVDDAIAERAVSLRQLH
RIKLPDAIIWATANVHSMLLITRNTKDFPREMPDIRVPYEI

Nucleotide

• Length: 366 bp

>T29890 NC_021911:c1062587-1062222 [Rhizobium etli bv. mimosae str. Mim1]
ATGGTAAAGTCTCTGTTCGACACTAATGTCTTGATCGATTATCTCAACGCAGTTCCACAAGCGCGAGACGAACTGAGGAG
ATATCCCGAAAAGGCGATCAGCATTATAACCTGGATGGAGGTTCTCGTCGGTGCCAAGCCTGAGGTGGCAATCGGAACGC
GCGCTTTCCTGGCCGGCTTTGCGGTCATCGCTGTCGATGACGCCATAGCCGAACGAGCAGTTTCTCTGCGACAACTTCAT
CGTATCAAGCTTCCAGATGCCATCATCTGGGCAACGGCCAATGTTCACTCGATGTTGCTGATCACCCGAAACACGAAGGA
TTTCCCTCGTGAAATGCCGGACATACGAGTGCCATACGAAATTTGA

Antitoxin

Protein

• Length: 72 a.a.
• Molecular weight: 8233.40 Da
• Isoelectric Point: 6.3273

>AT29890 WP_011428858.1 NC_021911:c1062796-1062581 [Rhizobium etli bv. mimosae str. Mim1]
MRTLVDIGDPEVKALDRLAQREKMSRAALIRKAINDFLARNNADIEAEAFGLWGDRKIDGLAYQENMRREW

Nucleotide

• Length: 216 bp

>AT29890 NC_021911:c1062796-1062581 [Rhizobium etli bv. mimosae str. Mim1]
ATGAGAACGTTGGTAGATATCGGCGACCCAGAAGTCAAAGCGCTGGATCGGCTGGCACAGCGGGAAAAAATGTCGAGAGC
AGCGCTGATCCGAAAGGCGATCAATGACTTCCTGGCTAGGAACAATGCCGATATCGAAGCAGAAGCGTTCGGGCTCTGGG
GCGATCGAAAGATCGATGGTTTGGCCTATCAGGAAAACATGCGCCGCGAATGGTAA

Structures

Toxin

• AlphaFold DB: S5SHE0

Antitoxin

• AlphaFold DB: S5SXW7