Detailed information of TA system TA148952

Bioinformatically predicted

Overview

TA module

• Type: II
• Classification (family/domain): vapBC/LOTUS_5_Limkain_b1-Phd
• Location: 63299..63990
• Replicon: plasmid pRle248e
• Accession: NZ_CP048281
• Organism: Rhizobium leguminosarum bv. viciae 248

Toxin (Protein)

• Gene name: vapC
• Uniprot ID: -
• Locus tag: GYN07_RS25420
• Protein ID: WP_020047055.1
• Coordinates: 63299..63727 (-)
• Length: 143 a.a.

Antitoxin (Protein)

• Gene name: vapB
• Uniprot ID: A0A4R0AD13
• Locus tag: GYN07_RS25425
• Protein ID: WP_017991284.1
• Coordinates: 63724..63990 (-)
• Length: 89 a.a.

Genomic Context

Locus tag	Coordinates	Strand	Size (bp)	Protein ID	Product	Description
GYN07_RS25385	58789..59436	+	648	WP_020047060.1	TetR/AcrR family transcriptional regulator	-
GYN07_RS25390	59442..59794	+	353	Protein_59	flagellar protein	-
GYN07_RS25395	59781..59976	+	196	Protein_60	hypothetical protein	-
GYN07_RS25400	60140..60979	+	840	WP_020047059.1	transporter substrate-binding domain-containing protein	-
GYN07_RS25405	61093..61755	+	663	WP_026264480.1	amino acid ABC transporter permease	-
GYN07_RS25410	61760..62419	+	660	WP_020047057.1	amino acid ABC transporter permease	-
GYN07_RS25415	62432..63202	+	771	WP_020047056.1	amino acid ABC transporter ATP-binding protein	-
GYN07_RS25420	63299..63727	-	429	WP_020047055.1	type II toxin-antitoxin system VapC family toxin	Toxin
GYN07_RS25425	63724..63990	-	267	WP_017991284.1	type II toxin-antitoxin system Phd/YefM family antitoxin	Antitoxin
GYN07_RS25430	64243..64992	+	750	WP_020047054.1	GntR family transcriptional regulator	-
GYN07_RS25435	64996..65781	+	786	WP_020047053.1	transporter substrate-binding domain-containing protein	-
GYN07_RS25440	65861..66532	+	672	WP_020047052.1	amino acid ABC transporter permease	-
GYN07_RS25445	66529..67188	+	660	WP_017956570.1	amino acid ABC transporter permease	-
GYN07_RS25450	67166..67891	+	726	WP_020047051.1	amino acid ABC transporter ATP-binding protein	-
GYN07_RS25455	68051..68422	-	372	WP_020047050.1	type II toxin-antitoxin system RelE/ParE family toxin	-
GYN07_RS25460	68422..68679	-	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..727585	727585

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: 15827.09 Da
• Isoelectric Point: 4.7981

>T148952 WP_020047055.1 NZ_CP048281:c63727-63299 [Rhizobium leguminosarum bv. viciae 248]
VRLLLDTNVLSEVTRPRPDARVLQWLDSLDEDRSFISIVSIAEIRRGVALMESGRKRDALSEWLAQDLPQRFEQRVIPVD
QPVAIAWGDLTGLAKRSGRGLSSMDGLIAATAIAHDLTLATRNIKDFEGLGIELVDPWTERP

Nucleotide

• Length: 429 bp

>T148952 NZ_CP063908:4230496-4230879 [Klebsiella pneumoniae]
ATGACCTCCGGATCTGCGCTTTTTGATACCAATATTCTTATTGATTTATTTAGCGGGCGTTGCGAAGCCAAACAGGCGCT
GGAGGCCTGGCCACCGCAGAATGCGATCAGTCTGATTACCTGGATGGAGGTGATGGTTGGCGCTAAAAAATATCACCAGG
AGCAGCGCACGCGAATGGCGCTGAGCACCTTTAATATCATTAACATCTCACAGGATATTGCAGAGCGAAGCGTTGCGCTG
CGGCAGGAGTATAAGCTTAAGCTGCCGGATGCCATCATTCTGGCGACGGCGCAACTCCATCGTCTGGAACTAATTACGCG
GAATACGAAGGGTTTTGCCGGTATTCCTGGCGTAGTCACGCCGTACGAAATCCACCCTGAATAA

Antitoxin

Protein

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

>AT148952 WP_017991284.1 NZ_CP048281:c63990-63724 [Rhizobium leguminosarum bv. viciae 248]
MQPSRPEDKSWTVASAKAKLSEVIERAQATPQTIMRNGKPSVVVVSAEEWQRKTARKGTLAEFLMQSPLRGADLDLERQR
DEPRDLQL

Nucleotide

• Length: 267 bp

>AT148952 NZ_CP063908:4230254-4230496 [Klebsiella pneumoniae]
ATGATGGCTGAAAGGGATATGGGCAGAATTCTTCTCGATTTATCAGACGATGTCATTCAACGTCTCGATGACCTCAAAGT
GCAGCGTAACATTCCGCGAGCGGAACTGTTACGTGAAGCGGTTGAACAATATCTGGAGAAACAAGATCGAGCTAAAGATA
CCATCTCCAGTGCGCTGGGTCTGTGGCAAGACTGCGAAGAAGACGGCATGGAATATCAACGTCAGCTACGCAAGGAGTGG
TAA

Structures

Antitoxin

• AlphaFold DB: A0A4R0AD13