Detailed information of TA system TA168613

Bioinformatically predicted

Overview

TA module

• Type: II
• Classification (family/domain): vagCD/VapC-VagC
• Location: 17449..18092
• Replicon: plasmid pKp46564-2QIL
• Accession: NZ_CP059315
• Organism: Klebsiella pneumoniae strain Kp46564

Toxin (Protein)

• Gene name: vagD
• Uniprot ID: D8L2J9
• Locus tag: H1D29_RS00395
• Protein ID: WP_001044770.1
• Coordinates: 17676..18092 (+)
• Length: 139 a.a.

Antitoxin (Protein)

• Gene name: vagC
• Uniprot ID: D5KTK7
• Locus tag: H1D29_RS00390
• Protein ID: WP_001261282.1
• Coordinates: 17449..17679 (+)
• Length: 77 a.a.

Genomic Context

Locus tag	Coordinates	Strand	Size (bp)	Protein ID	Product	Description
H1D29_RS00345	12647..13120	+	474	WP_004152341.1	YkgJ family cysteine cluster protein	-
H1D29_RS00350	13212..13442	+	231	WP_011977773.1	hypothetical protein	-
H1D29_RS00355	14334..15116	-	783	WP_004152340.1	site-specific integrase	-
H1D29_RS00360	15116..15448	-	333	WP_004152339.1	hypothetical protein	-
H1D29_RS00365	15455..15853	-	399	WP_004171440.1	hypothetical protein	-
H1D29_RS00370	15879..16208	-	330	WP_004152337.1	hypothetical protein	-
H1D29_RS00375	16236..16544	-	309	WP_004152336.1	hypothetical protein	-
H1D29_RS00380	16590..16796	-	207	WP_004153649.1	hypothetical protein	-
H1D29_RS00385	17031..17492	-	462	WP_072093212.1	hypothetical protein	-
H1D29_RS00390	17449..17679	+	231	WP_001261282.1	AbrB/MazE/SpoVT family DNA-binding domain-containing protein	Antitoxin
H1D29_RS00395	17676..18092	+	417	WP_001044770.1	type II toxin-antitoxin system VapC family toxin	Toxin
H1D29_RS00400	18166..18876	+	711	WP_004152334.1	ATP-binding protein	-
H1D29_RS00405	18910..19607	+	698	Protein_21	IS1 family transposase	-
H1D29_RS00410	19671..20081	+	411	WP_004152401.1	hypothetical protein	-
H1D29_RS00415	20738..21097	-	360	WP_117046906.1	DUF305 domain-containing protein	-
H1D29_RS00420	21269..21499	-	231	Protein_24	IS5/IS1182 family transposase	-
H1D29_RS00425	21601..22785	+	1185	WP_004152398.1	ISAs1-like element ISKpn31 family transposase	-

Associated MGEs

MGE detail	Similar MGEs	Relative position	MGE Type	Cargo ARG	Virulence gene	Coordinates	Length (bp)
	-	inside	Conjugative plasmid	blaKPC-2	-	1..101059	101059
	-	flank	IS/Tn	-	-	11259..12527	1268

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 (5-129)

Antitoxin

• SpoVT-AbrB domain (7-47)

Sequences

Toxin

Protein

• Length: 139 a.a.
• Molecular weight: 15106.52 Da
• Isoelectric Point: 7.1084

>T168613 WP_001044770.1 NZ_CP059315:17676-18092 [Klebsiella pneumoniae]
VNKTYMLDTCICSFIMREQPEAVLKRLEQAVLRGQRIVVSAITYSEMRFGATGPKASPRHVELVDAFCARLDAILPWDRA
AVDATTEIKVALRMAGTPIGPNDTAIAGHAIAAGAVLVTNNTREFERVPGLVLEDWVR

Nucleotide

• Length: 417 bp

>T168613 NZ_CP076136:4175258-4175623 [Bradyrhizobium sediminis]
ATGGTGAAAGCGCTGTTCGACACCAACATTCTCGTCGACTACCTCAATGCCGTTCCCCAGGCTCGCACTGAACTTCGACG
CTACACGGATAAAGCCGTCAGTATCATCACATGGATGGAGGTGATGGTTGGCGCTACCGACGATGTCGAGGAAACGACGC
GCGCCTTTCTGAGCACTTTCGATGTCATTGCGCTCGACGAAGCGATTGCAGAGCGCGCGGTCAGCCTGCGCCGCAACCAT
CACGTCAAATTGCCTGACGCCATTATCTGGGCAACGGCACAGGTCCACGCGATGCTTCTGGTCACACGAAAAACCAAGGA
CTTCACAGCCGGAGATCCTGGCGTCCGCATGCCCTACCGGCTCTAA

Antitoxin

Protein

• Length: 77 a.a.
• Molecular weight: 8756.83 Da
• Isoelectric Point: 4.4692

>AT168613 WP_001261282.1 NZ_CP059315:17449-17679 [Klebsiella pneumoniae]
MRTVSIFKNGNNRAIRLPRDLDFEGVSELEIVREGDSIILRPVRPTWGSFAQFEKADPDFMAEREDVVSDEGRFNL

Nucleotide

• Length: 231 bp

>AT168613 NZ_CP076136:4175049-4175264 [Bradyrhizobium sediminis]
ATGCGGACGCTGGTTGACCTCGGCAATAGCCAGATTCAAGCGCTGGACGAACTGTCAAAAAAGGAGAAGCGATCTCGCGC
GTCCCTGATCCGTCAGGCGATCGATGACTATCTCGGAAAGCGACGCGACAAGCAGGCAGGCGATGCGTTCGGCCTGTGGG
GCAAACGCAAGGTGGACGGCTTGGCCTATCAGGAAAAAGTGCGTGGCGAATGGTGA

Structures

Toxin

• AlphaFold DB: A0A0H3GYM2

Antitoxin

• AlphaFold DB: A0A0H3GZG3