Detailed information of TA system TA152247

Bioinformatically predicted

Overview

TA module

• Type: II
• Classification (family/domain): vapBC/LOTUS_5_Limkain_b1-Phd
• Location: 56182..56873
• Replicon: plasmid pRL9b4
• Accession: NZ_CP050098
• Organism: Rhizobium leguminosarum bv. trifolii strain 9B

Toxin (Protein)

• Gene name: vapC
• Uniprot ID: A0A6G8VST5
• Locus tag: HA461_RS24085
• Protein ID: WP_003562524.1
• Coordinates: 56182..56610 (-)
• Length: 143 a.a.

Antitoxin (Protein)

• Gene name: vapB
• Uniprot ID: A0A6G8VSU1
• Locus tag: HA461_RS24090
• Protein ID: WP_003562523.1
• Coordinates: 56607..56873 (-)
• Length: 89 a.a.

Genomic Context

Locus tag	Coordinates	Strand	Size (bp)	Protein ID	Product	Description
HA461_RS24065	53075..53914	+	840	WP_003562529.1	transporter substrate-binding domain-containing protein	-
HA461_RS24070	54032..54694	+	663	WP_028742556.1	amino acid ABC transporter permease	-
HA461_RS24075	54699..55358	+	660	WP_011648868.1	amino acid ABC transporter permease	-
HA461_RS24080	55371..56141	+	771	WP_003562525.1	amino acid ABC transporter ATP-binding protein	-
HA461_RS24085	56182..56610	-	429	WP_003562524.1	type II toxin-antitoxin system VapC family toxin	Toxin
HA461_RS24090	56607..56873	-	267	WP_003562523.1	type II toxin-antitoxin system Phd/YefM family antitoxin	Antitoxin
HA461_RS24095	57133..57876	+	744	WP_166471763.1	GntR family transcriptional regulator	-
HA461_RS24100	57880..58665	+	786	WP_003562521.1	transporter substrate-binding domain-containing protein	-
HA461_RS24105	58747..59418	+	672	WP_018073173.1	amino acid ABC transporter permease	-
HA461_RS24110	59415..60074	+	660	WP_003562519.1	amino acid ABC transporter permease	-
HA461_RS24115	60052..60777	+	726	WP_003562518.1	amino acid ABC transporter ATP-binding protein	-

Associated MGEs

MGE detail	Similar MGEs	Relative position	MGE Type	Cargo ARG	Virulence gene	Coordinates	Length (bp)
	-	inside	Non-Mobilizable plasmid	-	-	1..901131	901131

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

• Type II toxin-antitoxin system, antitoxin Phd/YefM (9-66)

Sequences

Toxin

Protein

• Length: 143 a.a.
• Molecular weight: 15812.09 Da
• Isoelectric Point: 4.7948

>T152247 WP_003562524.1 NZ_CP050098:c56610-56182 [Rhizobium leguminosarum bv. trifolii]
VRLLLDTNVLSEVTRPRPDAHVLQWLDSLDEDRSFISVVSIAEIRRGVALMESGRKRDALAEWLAQDLPQRFEQRVIPVD
QPVAIAWGDLMGLAKRSGRGLSSMDGLIAATAIAHDLTLATRNIKDFEGFGIELVDPWAERP

Nucleotide

• Length: 429 bp

>T152247 NZ_CP066075:c3611775-3611494 [Paraburkholderia ginsengisoli]
ATGATCACGACATTCGGCGACAAGGCTACGGCGAGAATCTTCCAGGGCAAGTTCGTGCATTCACTGCCGCTTCACATCCA
GGCGCTCGCGCGCCGCAAGCTGCTGATGATCGACGCCGCCGATTCCATCGCCAATCTGCACGCGCCGCCCGGCAACCGGC
TCGAAGCCTTGCAGGGACAGCGCAGCGGGCAATGGAGCATCCGGATCAATGCGCAATGGCGCATCTGTTTCCACTTCGTC
GGCGAGGAGGCGCTGAATGTCGAGATTGTCGACTATCACTGA

Antitoxin

Protein

• Length: 89 a.a.
• Molecular weight: 9994.36 Da
• Isoelectric Point: 10.0842

>AT152247 WP_003562523.1 NZ_CP050098:c56873-56607 [Rhizobium leguminosarum bv. trifolii]
MQPSRPEDKSWTVASAKAKLSEVIERAQATPQTIMRNGKPSVVVVSAEEWQRKTARKGTLAEFLMQSPLRGADLDLERQR
DEPRDFQL

Nucleotide

• Length: 267 bp

>AT152247 NZ_CP066075:c3611477-3611022 [Paraburkholderia ginsengisoli]
ATGGTCATCAAACGCTCGTCGCTCGGCAGCATCGATTTCTCGGACATCGATACCGGGGACAACATCCCGGAAATCCATCC
GGGCGAAATTCTGCGCAGCGAGTTCCTCGAACCGCTCGGCATGTCCGTCAATGCGCTCGCGCTCGCGCTGCGTGTGCCGG
CGCCGCGCATCAACGACGTCGTGCGCGGCAAGCGCGCCATCTCGGCGGATACCGCGCTGCGGCTCGAGCGCTACTTCGGC
GCGAGCGCGCCATTCTGGCTCAACCTGCAGATCGCCTACGACCTGCGCGTCGCCACCGCGGCGGCCGGCGAGCAGATCGA
ACGCGAGATCGAACCCATGCCCAAATCAGACCGCCCGAAAATGCCGAAGGTGTCGGCCGAACATACCCGGGCCGCGGCGC
TCGCGGTCAGCGTGAGCGGCAGTCACACTGCCGGCAAGGCGCGCCGCAAAGCCTGA

Structures

Toxin

• AlphaFold DB: A0A6G8VST5

Antitoxin

• AlphaFold DB: A0A6G8VSU1