Detailed information of TA system TA115459

Bioinformatically predicted

Overview

TA module

• Type: II
• Classification (family/domain): vapBC/VapC-VapB
• Location: 1949400..1949965
• Replicon: chromosome
• Accession: NZ_CP034179
• Organism: Novosphingobium tardaugens NBRC 16725

Toxin (Protein)

• Gene name: vapC
• Uniprot ID: U2YKN1
• Locus tag: EGO55_RS09020
• Protein ID: WP_021689749.1
• Coordinates: 1949594..1949965 (+)
• Length: 124 a.a.

Antitoxin (Protein)

• Gene name: vapB
• Uniprot ID: U3A286
• Locus tag: EGO55_RS09015
• Protein ID: WP_021689750.1
• Coordinates: 1949400..1949597 (+)
• Length: 66 a.a.

Genomic Context

Locus tag	Coordinates	Strand	Size (bp)	Protein ID	Product	Description
EGO55_RS08985	1944939..1945199	+	261	WP_021689756.1	hypothetical protein	-
EGO55_RS08990	1945196..1945672	+	477	WP_021689755.1	DUF2840 domain-containing protein	-
EGO55_RS08995	1945669..1946250	+	582	WP_021689754.1	S26 family signal peptidase	-
EGO55_RS09000	1946219..1946554	+	336	WP_021689753.1	DUF736 domain-containing protein	-
EGO55_RS09005	1946559..1947287	+	729	WP_021689752.1	lytic transglycosylase domain-containing protein	-
EGO55_RS09010	1947541..1949304	+	1764	WP_021689751.1	VirD2 family relaxase/mobilization nuclease	-
EGO55_RS09015	1949400..1949597	+	198	WP_021689750.1	type II toxin-antitoxin system VapB family antitoxin	Antitoxin
EGO55_RS09020	1949594..1949965	+	372	WP_021689749.1	type II toxin-antitoxin system VapC family toxin	Toxin
EGO55_RS09025	1950365..1952362	+	1998	WP_021689748.1	conjugal transfer protein TraG	-
EGO55_RS09030	1952379..1952816	+	438	WP_021689747.1	hypothetical protein	-
EGO55_RS09035	1953005..1953979	+	975	WP_052023650.1	P-type conjugative transfer ATPase TrbB	-
EGO55_RS09040	1953976..1954308	+	333	WP_021689745.1	TrbC/VirB2 family protein	-
EGO55_RS09045	1954308..1954580	+	273	WP_021689744.1	VirB3 family type IV secretion system protein	-

Associated MGEs

MGE detail	Similar MGEs	Relative position	MGE Type	Cargo ARG	Virulence gene	Coordinates	Length (bp)
	-	inside	Integrative and Conjugative Element	-	-	1922818..1983119	60301

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

No domain identified.

Antitoxin

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

Sequences

Toxin

Protein

• Length: 124 a.a.
• Molecular weight: 13753.84 Da
• Isoelectric Point: 6.0752

>T115459 WP_021689749.1 NZ_CP034179:1949594-1949965 [Novosphingobium tardaugens NBRC 16725]
MILVDSTIWVDHLRRTDPALVERLNAGVVFIHPFIIGEIALGSLRQRDVVLSSLRGLPGATQATDDEVQTFIEQQPLYSL
GIGYIDAHLLTSVRLTPGMRLWTRDRRLNEIATRLGVAEVAEH

Nucleotide

• Length: 372 bp

>T115459 NZ_CP034179:1949594-1949965 [Novosphingobium tardaugens NBRC 16725]
ATGATCCTGGTCGACAGCACGATTTGGGTCGACCACTTGCGGCGGACTGATCCAGCGCTCGTAGAGCGGCTGAATGCAGG
TGTTGTATTCATCCACCCGTTCATCATCGGCGAGATCGCGCTAGGCAGTCTGCGCCAGCGGGATGTGGTGCTATCCAGCT
TGCGCGGGCTGCCAGGAGCAACGCAAGCGACCGACGATGAGGTGCAGACCTTCATTGAGCAGCAGCCCCTGTACAGCCTC
GGCATCGGTTACATCGACGCGCACCTCCTTACGTCCGTACGGCTCACCCCAGGAATGCGGCTGTGGACACGAGACCGGAG
ACTGAATGAAATCGCGACACGTCTCGGCGTGGCAGAAGTCGCCGAACATTGA

Antitoxin

Protein

• Length: 66 a.a.
• Molecular weight: 7271.37 Da
• Isoelectric Point: 8.8337

>AT115459 WP_021689750.1 NZ_CP034179:1949400-1949597 [Novosphingobium tardaugens NBRC 16725]
MRTTIVLDDDLLAKAQAFTGLKEKSQLVREAFKALIERESARRLALLGGSESDLELPTRRRSVAE

Nucleotide

• Length: 198 bp

>AT115459 NZ_CP034179:1949400-1949597 [Novosphingobium tardaugens NBRC 16725]
ATGCGCACGACCATCGTGTTGGATGATGATTTGCTCGCCAAGGCTCAGGCCTTCACCGGGCTCAAGGAAAAGTCGCAGCT
TGTGCGCGAAGCCTTCAAAGCGCTCATCGAACGCGAAAGCGCGCGGCGGCTTGCGTTGCTCGGCGGGAGCGAGTCTGATC
TTGAGCTTCCGACGCGTCGCCGCTCGGTTGCGGAATGA

Structures

Toxin

• AlphaFold DB: U2YKN1

Antitoxin

• AlphaFold DB: U3A286