Detailed information of TA system TA076018

Bioinformatically predicted

Overview

TA module

• Type: II
• Classification (family/domain): vapBC/VapC-VapB
• Location: 31973..32553
• Replicon: plasmid pRetKim5a
• Accession: NZ_CP021125
• Organism: Rhizobium sp. Kim5

Toxin (Protein)

• Gene name: vapC
• Uniprot ID: A0A7U4IV52
• Locus tag: KIM5_RS22705
• Protein ID: WP_040111689.1
• Coordinates: 31973..32356 (-)
• Length: 128 a.a.

Antitoxin (Protein)

• Gene name: vapB
• Uniprot ID: A0A7W6MIA3
• Locus tag: KIM5_RS22710
• Protein ID: WP_016736583.1
• Coordinates: 32353..32553 (-)
• Length: 67 a.a.

Genomic Context

Locus tag	Coordinates	Strand	Size (bp)	Protein ID	Product	Description
KIM5_RS34335	26991..27164	-	174	WP_009987945.1	hypothetical protein	-
KIM5_RS22670	27219..27470	-	252	WP_009987947.1	hypothetical protein	-
KIM5_RS22675	27630..28343	-	714	Protein_24	Ku protein	-
KIM5_RS22680	28542..28718	+	177	WP_086156492.1	hypothetical protein	-
KIM5_RS33820	28859..28987	-	129	Protein_26	phenylalanine 4-monooxygenase	-
KIM5_RS34340	28970..29281	+	312	Protein_27	DNA polymerase Y family protein	-
KIM5_RS34345	29282..29725	+	444	Protein_28	error-prone DNA polymerase	-
KIM5_RS22690	30053..30664	-	612	WP_125461999.1	hypothetical protein	-
KIM5_RS33825	30661..31008	-	348	WP_164519056.1	hypothetical protein	-
KIM5_RS33835	31299..31421	+	123	Protein_31	secretion protein HlyD	-
KIM5_RS33840	31364..31686	-	323	Protein_32	MerR family DNA-binding transcriptional regulator	-
KIM5_RS22705	31973..32356	-	384	WP_040111689.1	type II toxin-antitoxin system VapC family toxin	Toxin
KIM5_RS22710	32353..32553	-	201	WP_016736583.1	type II toxin-antitoxin system VapB family antitoxin	Antitoxin
KIM5_RS22715	32911..33327	+	417	WP_009989135.1	response regulator	-
KIM5_RS22720	33338..33673	-	336	WP_086156497.1	response regulator	-
KIM5_RS22725	33804..34367	-	564	WP_086156498.1	DUF4142 domain-containing protein	-
KIM5_RS22730	34440..34631	-	192	WP_009986110.1	hypothetical protein	-
KIM5_RS22740	35634..37532	+	1899	Protein_39	PAS domain S-box protein	-

Associated MGEs

MGE detail	Similar MGEs	Relative position	MGE Type	Cargo ARG	Virulence gene	Coordinates	Length (bp)
	-	inside	Conjugative plasmid	-	hsiC1/vipB	1..431886	431886

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 (2-113)

Antitoxin

• Bacterial antitoxin of type II TA system, VapB (1-42)

Sequences

Toxin

Protein

• Length: 128 a.a.
• Molecular weight: 14204.34 Da
• Isoelectric Point: 6.8446

>T76018 WP_040111689.1 NZ_CP021125:c32356-31973 [Rhizobium sp. Kim5]
VILADTSIWIDHFRHADSELRRIIEDDRLLCHPAVIGELALGSLRDRSSVMAFLAAQREAFVATHDEVMMMIDRHAIFSM
GIGYTDAHLMASVLLDQRAVLWTRDKRLRAAAEKAGASLHTPANARN

Nucleotide

• Length: 384 bp

>T76018 NZ_CP021125:c32356-31973 [Rhizobium sp. Kim5]
GTGATACTTGCCGACACTTCCATCTGGATCGATCATTTCCGGCACGCCGATTCAGAGCTGCGTAGGATTATTGAGGACGA
TCGTCTCTTATGCCATCCAGCCGTAATCGGAGAGCTCGCACTTGGCAGCCTTCGGGATCGCAGTAGCGTGATGGCTTTCC
TGGCGGCCCAGCGCGAAGCGTTCGTCGCGACGCACGACGAAGTTATGATGATGATTGATCGCCACGCCATTTTCAGTATG
GGCATTGGCTATACAGATGCCCACTTGATGGCCTCAGTTCTCCTCGATCAACGAGCGGTCTTATGGACCAGAGACAAGCG
TCTGCGGGCAGCGGCCGAAAAGGCGGGGGCTTCATTGCACACCCCTGCCAACGCGCGAAACTAA

Antitoxin

Protein

• Length: 67 a.a.
• Molecular weight: 7154.26 Da
• Isoelectric Point: 11.3760

>AT76018 WP_016736583.1 NZ_CP021125:c32553-32353 [Rhizobium sp. Kim5]
MRSTINLDDTLMERARSLTGTKETATLVRQALETLVRVESGKRLIALGGTMPDAEAAPRRRSAAAK

Nucleotide

• Length: 201 bp

>AT76018 NZ_CP021125:c32553-32353 [Rhizobium sp. Kim5]
ATGCGATCGACTATCAATCTCGACGACACCCTCATGGAAAGGGCTAGGTCTCTAACGGGCACGAAAGAAACCGCCACTCT
GGTCCGCCAAGCGTTGGAGACGCTTGTTCGTGTGGAGTCGGGAAAACGCCTCATCGCGCTTGGCGGAACTATGCCGGATG
CGGAGGCAGCCCCACGCCGCCGGAGCGCAGCCGCCAAGTGA

Structures

Toxin

• AlphaFold DB: A0A7U4IV52

Antitoxin

• AlphaFold DB: A0A7W6MIA3