Detailed information of TA system TA023900

Bioinformatically predicted

Overview

TA module

• Type: II
• Classification (family/domain): vapBC/LOTUS_5_Limkain_b1-Phd
• Location: 675737..676428
• Replicon: plasmid pR132501
• Accession: NC_012848
• Organism: Rhizobium leguminosarum bv. trifolii WSM1325

Toxin (Protein)

• Gene name: vapC
• Uniprot ID: C6B5W1
• Locus tag: RLEG_RS26075
• Protein ID: WP_012755577.1
• Coordinates: 675737..676165 (-)
• Length: 143 a.a.

Antitoxin (Protein)

• Gene name: vapB
• Uniprot ID: C6B5W2
• Locus tag: RLEG_RS26080
• Protein ID: WP_012755578.1
• Coordinates: 676162..676428 (-)
• Length: 89 a.a.

Genomic Context

Locus tag	Coordinates	Strand	Size (bp)	Protein ID	Product	Description
RLEG_RS26045	670886..671689	-	804	WP_012755571.1	crotonase/enoyl-CoA hydratase family protein	-
RLEG_RS26050	671778..672362	+	585	WP_012755572.1	TetR/AcrR family transcriptional regulator	-
RLEG_RS38200	672458..672634	-	177	WP_157628365.1	hypothetical protein	-
RLEG_RS26055	672633..673472	+	840	WP_012755573.1	transporter substrate-binding domain-containing protein	-
RLEG_RS26060	673590..674252	+	663	WP_012755574.1	amino acid ABC transporter permease	-
RLEG_RS26065	674258..674917	+	660	WP_012755575.1	amino acid ABC transporter permease	-
RLEG_RS26070	674930..675700	+	771	WP_012755576.1	amino acid ABC transporter ATP-binding protein	-
RLEG_RS26075	675737..676165	-	429	WP_012755577.1	type II toxin-antitoxin system VapC family toxin	Toxin
RLEG_RS26080	676162..676428	-	267	WP_012755578.1	type II toxin-antitoxin system prevent-host-death family antitoxin	Antitoxin
RLEG_RS36365	676687..677370	+	684	Protein_614	GntR family transcriptional regulator	-
RLEG_RS26090	677441..678226	+	786	WP_012755579.1	transporter substrate-binding domain-containing protein	-
RLEG_RS26095	678306..678977	+	672	WP_012755580.1	amino acid ABC transporter permease	-
RLEG_RS26100	678974..679633	+	660	WP_011648875.1	amino acid ABC transporter permease	-
RLEG_RS26105	679611..680336	+	726	WP_012755581.1	amino acid ABC transporter ATP-binding protein	-
RLEG_RS26110	680610..680978	-	369	Protein_619	type II toxin-antitoxin system RelE/ParE family toxin	-
RLEG_RS26115	680978..681235	-	258	WP_003550229.1	hypothetical protein	-

Associated MGEs

MGE detail	Similar MGEs	Relative position	MGE Type	Cargo ARG	Virulence gene	Coordinates	Length (bp)
	-	inside	Non-Mobilizable plasmid	-	-	1..828924	828924

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 (3-123)

Antitoxin

• Type II toxin-antitoxin system, antitoxin Phd/YefM (9-67)

Sequences

Toxin

Protein

• Length: 143 a.a.
• Molecular weight: 15826.12 Da
• Isoelectric Point: 6.0930

>T23900 WP_012755577.1 NC_012848:c676165-675737 [Rhizobium leguminosarum bv. trifolii WSM1325]
VRVLLDTNVLSEVTRPRPDAHVLQWLDSLDEDRSFISTVSIAEIRRGVALMESGRKRDALAEWLAQDLPQRFEQRVIPVH
QPVAIAWGDLMGLAKRSGRGLSSMDGLIGATAIAHDLTLATRNIKDFEGLGIELVHPWTERP

Nucleotide

• Length: 429 bp

>T23900 NC_012848:c676165-675737 [Rhizobium leguminosarum bv. trifolii WSM1325]
GTGAGAGTTCTGCTCGACACCAATGTGCTTTCCGAGGTGACAAGGCCGCGTCCCGATGCACATGTCTTACAATGGCTGGA
CAGTCTCGACGAGGATCGCTCATTCATCAGCACCGTATCGATCGCGGAGATCCGGCGTGGTGTCGCATTGATGGAAAGCG
GGCGAAAGCGCGACGCGCTGGCTGAATGGCTTGCCCAGGATCTGCCGCAGCGCTTCGAGCAGCGCGTCATCCCTGTGCAC
CAGCCGGTTGCGATAGCCTGGGGCGACCTGATGGGGCTCGCAAAGCGAAGCGGACGCGGCTTATCGTCAATGGACGGCTT
AATTGGCGCCACCGCGATTGCTCACGATCTCACCCTCGCCACGCGCAATATAAAGGATTTCGAGGGCCTTGGGATCGAGC
TTGTCCACCCTTGGACCGAGCGCCCGTGA

Antitoxin

Protein

• Length: 89 a.a.
• Molecular weight: 9960.34 Da
• Isoelectric Point: 10.0842

>AT23900 WP_012755578.1 NC_012848:c676428-676162 [Rhizobium leguminosarum bv. trifolii WSM1325]
MQPSRPEDKSWTVASAKAKLSEVIQRAQATPQTIMRNGKPSVVVVSAEEWQRKTARKGTLAEFLMQSPLRGADLDLERER
DEPRDLQL

Nucleotide

• Length: 267 bp

>AT23900 NC_012848:c676428-676162 [Rhizobium leguminosarum bv. trifolii WSM1325]
ATGCAGCCATCACGACCAGAGGATAAAAGTTGGACCGTCGCCAGTGCGAAGGCCAAACTGTCTGAGGTTATCCAACGCGC
GCAAGCAACGCCGCAAACGATCATGCGCAATGGTAAACCAAGCGTCGTCGTCGTTTCAGCCGAGGAATGGCAGCGGAAGA
CCGCGCGCAAGGGCACCCTCGCAGAGTTTCTGATGCAATCGCCGCTGCGGGGCGCCGATCTCGATCTCGAGCGTGAACGC
GACGAACCGCGTGATCTCCAGCTGTGA

Structures

Toxin

• AlphaFold DB: C6B5W1

Antitoxin

• AlphaFold DB: C6B5W2