Detailed information of TA system TA076024

Bioinformatically predicted

Overview

TA module

• Type: II
• Classification (family/domain): vapBC/LOTUS_5_Limkain_b1-Phd
• Location: 611608..612293
• Replicon: plasmid pRetKim5d
• Accession: NZ_CP021128
• Organism: Rhizobium sp. Kim5

Toxin (Protein)

• Gene name: vapC
• Uniprot ID: A0A060IDY5
• Locus tag: KIM5_RS33020
• Protein ID: WP_040113056.1
• Coordinates: 611871..612293 (+)
• Length: 141 a.a.

Antitoxin (Protein)

• Gene name: vapB
• Uniprot ID: -
• Locus tag: KIM5_RS33015
• Protein ID: WP_086156759.1
• Coordinates: 611608..611874 (+)
• Length: 89 a.a.

Genomic Context

Locus tag	Coordinates	Strand	Size (bp)	Protein ID	Product	Description
KIM5_RS32995	607223..608275	+	1053	WP_086156756.1	iron ABC transporter permease	-
KIM5_RS33000	608272..609060	+	789	WP_086156757.1	ABC transporter ATP-binding protein	-
KIM5_RS33005	609089..609517	-	429	WP_086156758.1	MarR family transcriptional regulator	-
KIM5_RS33010	609724..611535	+	1812	WP_040143122.1	chloride channel protein	-
KIM5_RS33015	611608..611874	+	267	WP_086156759.1	type II toxin-antitoxin system prevent-host-death family antitoxin	Antitoxin
KIM5_RS33020	611871..612293	+	423	WP_040113056.1	type II toxin-antitoxin system VapC family toxin	Toxin
KIM5_RS33025	612319..613089	-	771	WP_086156760.1	ABC transporter ATP-binding protein	-
KIM5_RS33030	613099..614082	-	984	WP_040143127.1	ABC transporter substrate-binding protein	-
KIM5_RS33035	614121..614972	-	852	WP_009992575.1	ABC transporter permease	-
KIM5_RS33040	614983..616335	-	1353	WP_040113060.1	LLM class flavin-dependent oxidoreductase	-

Associated MGEs

MGE detail	Similar MGEs	Relative position	MGE Type	Cargo ARG	Virulence gene	Coordinates	Length (bp)
	-	inside	Conjugative plasmid	-	-	1..684601	684601

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 (4-125)

Antitoxin

• Type II toxin-antitoxin system, antitoxin Phd/YefM (9-63)

Sequences

Toxin

Protein

• Length: 141 a.a.
• Molecular weight: 15617.02 Da
• Isoelectric Point: 4.6791

>T76024 WP_040113056.1 NZ_CP021128:611871-612293 [Rhizobium sp. Kim5]
VRLLLDTNVLLEVTKPNPEMRVLAWLDKLDEDRSFISIVSVAEIRRGVALMDEGRKRDALAEWLARDLPQRFEGRIIPMD
EPVALAWGDLMGPAKRNGRGLSSIDGLIAATAVAHDLTLATRNTRDFEGFGIELIDPWIA

Nucleotide

• Length: 423 bp

>T76024 NZ_CP021128:611871-612293 [Rhizobium sp. Kim5]
GTGAGGCTTCTGCTGGACACCAACGTGCTGTTGGAGGTGACGAAGCCGAACCCCGAAATGCGCGTCTTGGCTTGGCTGGA
TAAGCTGGATGAGGATCGCTCCTTCATCAGCATCGTGTCTGTCGCGGAGATCCGGCGCGGTGTTGCCCTGATGGACGAGG
GACGAAAACGCGACGCGCTGGCCGAATGGCTTGCCCGGGACCTGCCGCAACGCTTCGAGGGCCGCATCATTCCGATGGAC
GAGCCGGTTGCCTTAGCCTGGGGTGACCTTATGGGCCCCGCGAAGCGGAACGGCCGCGGCCTGTCGTCGATAGATGGACT
GATCGCTGCAACCGCGGTTGCTCACGATCTCACTCTCGCCACGCGCAACACCAGGGATTTCGAGGGGTTCGGGATCGAAC
TCATCGATCCCTGGATCGCATAG

Antitoxin

Protein

• Length: 89 a.a.
• Molecular weight: 9820.01 Da
• Isoelectric Point: 8.7841

>AT76024 WP_086156759.1 NZ_CP021128:611608-611874 [Rhizobium sp. Kim5]
MRPSRQGDESWTVASAKAKLSEVIERAQSAPQTITRNGKPSVVVVSGEEWQRKTARKGTLAEFLMSSPLRGADLDLERQR
DDPRDPEL

Nucleotide

• Length: 267 bp

>AT76024 NZ_CP021128:611608-611874 [Rhizobium sp. Kim5]
ATGCGACCGTCACGGCAAGGCGATGAAAGCTGGACCGTCGCCAGCGCAAAGGCAAAGCTTTCCGAGGTTATCGAACGCGC
GCAATCCGCGCCGCAAACGATTACCCGGAACGGCAAGCCGAGCGTCGTCGTCGTCTCCGGCGAGGAGTGGCAGCGCAAGA
CTGCGCGCAAGGGTACGCTTGCCGAATTCCTGATGAGTTCGCCGCTGCGTGGCGCCGATCTGGATCTCGAGCGTCAACGC
GACGATCCGCGTGATCCCGAACTGTGA

Structures

Toxin

• AlphaFold DB: A0A060IDY5