Detailed information of TA system TA170026

Bioinformatically predicted

Overview

TA module

• Type: II
• Classification (family/domain): vapBC/LOTUS_5_Limkain_b1-VagC
• Location: 2460055..2460693
• Replicon: chromosome
• Accession: NZ_CP060122
• Organism: Sphingobium yanoikuyae strain A3

Toxin (Protein)

• Gene name: vapC
• Uniprot ID: -
• Locus tag: H3V42_RS11980
• Protein ID: WP_048938827.1
• Coordinates: 2460292..2460693 (+)
• Length: 134 a.a.

Antitoxin (Protein)

• Gene name: vapB
• Uniprot ID: A0A0J9FLQ9
• Locus tag: H3V42_RS11975
• Protein ID: WP_010338822.1
• Coordinates: 2460055..2460288 (+)
• Length: 78 a.a.

Genomic Context

Locus tag	Coordinates	Strand	Size (bp)	Protein ID	Product	Description
H3V42_RS11940	2455842..2456267	+	426	WP_159365878.1	PRTRC system protein E	-
H3V42_RS11945	2456322..2456528	+	207	WP_159365879.1	hypothetical protein	-
H3V42_RS11950	2456540..2456767	+	228	WP_169860753.1	hypothetical protein	-
H3V42_RS11955	2456871..2457728	+	858	Protein_2353	hypothetical protein	-
H3V42_RS11960	2457740..2458570	+	831	WP_159365880.1	PRTRC system protein B	-
H3V42_RS11965	2458567..2459226	+	660	WP_159365881.1	PRTRC system protein A	-
H3V42_RS11970	2459216..2460019	+	804	WP_159365882.1	PRTRC system ThiF family protein	-
H3V42_RS11975	2460055..2460288	+	234	WP_010338822.1	AbrB/MazE/SpoVT family DNA-binding domain-containing protein	Antitoxin
H3V42_RS11980	2460292..2460693	+	402	WP_048938827.1	type II toxin-antitoxin system VapC family toxin	Toxin
H3V42_RS11985	2460885..2462255	+	1371	WP_159365883.1	hypothetical protein	-
H3V42_RS11990	2462786..2463871	+	1086	WP_159365884.1	DUF4297 domain-containing protein	-
H3V42_RS11995	2463929..2465617	+	1689	WP_159365885.1	hypothetical protein	-

Associated MGEs

MGE detail	Similar MGEs	Relative position	MGE Type	Cargo ARG	Virulence gene	Coordinates	Length (bp)

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 (3-123)

Antitoxin

• SpoVT-AbrB domain (10-55)

Sequences

Toxin

Protein

• Length: 134 a.a.
• Molecular weight: 14437.62 Da
• Isoelectric Point: 4.7363

>T170026 WP_048938827.1 NZ_CP060122:2460292-2460693 [Sphingobium yanoikuyae]
MFLLDTNILSDLIRQPDGMVAHAIADVGEDAVATSIIVAGELRYGAEKRGSPRLKSKIEDLLSLIAVLPLKDDADACYGR
LRADLERRGTPIGANDMLIAAHALAIGATLVTDNIREFERVDGLQLVNWLRTT

Nucleotide

• Length: 402 bp

>T170026 NZ_CP077061:c2740-2207 [Vibrio cholerae]
GTGAGTTGGGGCAAAGAGTTTGTAGAACTTAGTAAATCAAAGCATGACCGCGACTCATTTGACTGTGGTGAGCAAGAGCT
AAACACATTTATCAAAACTCAAGCTGCAAAGCACATGCAAGCAGGTATTAGCCGAACAATGGTTTTACCTAGTGCTCACC
CACTGTTAAATCAAAAATTCGCTATTTGTGCCTTTTATAGTGTTGCACCGAGCTCAATCAGCCGAGAAACATTACCGGCA
CAATTAGCAAAGAAACTACCGAGGTATCCAATCCCTGTTTTTCTGTTGGCTCAGTTAGCTGTGCACAAAGAATTTCACGG
TTCTGGACTTGGAAAGGTCAGTCTAATCCGTGCGCTGAAGTACTTGTGGGAAGTGAATCATCACATGAGAGCATACGCAA
TAGTTGTGGATTGTCTGACAGATTCCGCTCAAGCGTTCTATACGAAGTTCGGCTTTGAAGTATTGTGCGAACATAATGAG
CGTATTCGTATGTTCTTACCGATGAAAACGGTAGAACAACTTTTTAATCAATAG

Antitoxin

Protein

• Length: 78 a.a.
• Molecular weight: 8809.19 Da
• Isoelectric Point: 4.8723

>AT170026 WP_010338822.1 NZ_CP060122:2460055-2460288 [Sphingobium yanoikuyae]
MNLERHVKLFKNGRSQAVRIPREFELPGEDAIIRKEGSRLIIEPARPRSLLAVLKTWEPLDEEIGPIEDLPAEPVDI

Nucleotide

• Length: 234 bp

>AT170026 NZ_CP077061:c3006-2737 [Vibrio cholerae]
ATGGCAACGGCACGTTTAGATATCCGCCTTGATGAAGAGATCAAGGCAAAAGCTGAAAAGGCATCGGCTTTACTTGGTTT
AAAAAGTCTCACTGAATATGTGGTGAGACTTATGGACGAAGATGCGACTCATGTTATTGAGGAGCATGAAAGTATTATGG
TTAAAGACAGTGTTTTTGACGAGTTTATGGCTGCGTGTAATAAAGTAAAAGCACCGAATCAAGCTTTGCTTGAAGCTGTT
AAATTTACAGAGAAGAGCGGTATCAAGTGA

Structures

Antitoxin

• AlphaFold DB: A0A0J9FLQ9