Detailed information of TA system TA219775

Bioinformatically predicted

Overview

TA module

• Type: II
• Classification (family/domain): yafN-yafO (relBE)/YafO-YafN
• Location: 1004404..1005098
• Replicon: chromosome
• Accession: NZ_CP084879
• Organism: Shigella flexneri strain CMCC51574

Toxin (Protein)

• Gene name: yafO
• Uniprot ID: Q0T7Q5
• Locus tag: LGV73_RS04965
• Protein ID: WP_001263491.1
• Coordinates: 1004700..1005098 (+)
• Length: 133 a.a.

Antitoxin (Protein)

• Gene name: yafN
• Uniprot ID: Q0T7Q4
• Locus tag: LGV73_RS04960
• Protein ID: WP_000554759.1
• Coordinates: 1004404..1004697 (+)
• Length: 98 a.a.

Genomic Context

Locus tag	Coordinates	Strand	Size (bp)	Protein ID	Product	Description
LGV73_RS04940 (1000043)	1000043..1000540	+	498	WP_000006251.1	REP-associated tyrosine transposase RayT	-
LGV73_RS04945 (1000757)	1000757..1002469	-	1713	Protein_970	flagellar biosynthesis protein FlhA	-
LGV73_RS04950 (1002441)	1002441..1003226	+	786	WP_000207561.1	putative lateral flagellar export/assembly protein LafU	-
LGV73_RS04955 (1003297)	1003297..1004352	+	1056	WP_001226172.1	DNA polymerase IV	-
LGV73_RS04960 (1004404)	1004404..1004697	+	294	WP_000554759.1	type I toxin-antitoxin system antitoxin YafN	Antitoxin
LGV73_RS04965 (1004700)	1004700..1005098	+	399	WP_001263491.1	type II toxin-antitoxin system mRNA interferase toxin YafO	Toxin
LGV73_RS04970 (1005108)	1005108..1005560	+	453	WP_001059861.1	GNAT family N-acetyltransferase	-
LGV73_RS04975 (1005806)	1005806..1006849	+	1044	WP_005060486.1	RNA ligase RtcB family protein	-
LGV73_RS04980 (1006965)	1006965..1007525	+	561	Protein_977	peptide chain release factor H	-
LGV73_RS04985 (1007582)	1007582..1009039	-	1458	WP_001293009.1	cytosol nonspecific dipeptidase	-
LGV73_RS04990 (1009301)	1009301..1009759	+	459	WP_001291990.1	xanthine phosphoribosyltransferase	-

Associated MGEs

MGE detail	Similar MGEs	Relative position	MGE Type	Cargo ARG	Virulence gene	Coordinates	Length (bp)
	-	inside	Prophage	-	gmhA/lpcA / gtrII / gtrB / gtrA / gtrB	924739..1078639	153900
	-	inside	Prophage	-	gtrII / gtrB / gtrA / gtrB	998222..1083232	85010

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

• mRNA interferase toxin YafO (27-130)

Antitoxin

No domain identified.

Sequences

Toxin

Protein

• Length: 133 a.a.
• Molecular weight: 15457.86 Da
• Isoelectric Point: 8.0949

>T219775 WP_001263491.1 NZ_CP084879:1004700-1005098 [Shigella flexneri]
MRVFKTKLIRLQLTAEELDALTADFISYKRDGVLPDIFGRDALYDDSFTWPLIKFERVAHIHLANVNNPFPPQLRQFSRT
NDEAHLVYCQGAFDEQAWLLIAILKPEPHKLARDNNQMHKIGKMAEAFRMRF

Nucleotide

• Length: 399 bp

>T219775 NZ_CP116702:132733-133026 [Agrobacterium fabacearum]
ATGCCATTTAGCCTATCTGTCCAAGCGGAAGAGGATATTATTTCCATTGCAGAAGAAGGCATCCGCATCTTCGGAGCACT
AGTCGCCAGACAATATCACGATGAGCTTTTTGCCTTGCTCGAACTCATCGCCACCAACCCAAGAATGGCACGCGAAAGCC
ATGAGATTTCTCCTCCTGTCAGGATCCATCCTTTCAAGGCTCACCTTGTCGTGTACCGCGTCATTGAAGACGGGAGCGTA
TTCGTCATCCGCATACGTCACGGCCATGAAGATTGGGCGGGAGATTCTTTCTAA

Antitoxin

Protein

• Length: 98 a.a.
• Molecular weight: 11232.82 Da
• Isoelectric Point: 7.0153

>AT219775 WP_000554759.1 NZ_CP084879:1004404-1004697 [Shigella flexneri]
MHRILAEKSVNITELRKNPAKYFIDQPVAVLSNNRPAGYLLSASAFEALMDMLAEQEEKKPIKARFRPSAARLEEITRRA
KQYLNDMTDDDFNDFKE

Nucleotide

• Length: 294 bp

>AT219775 NZ_CP116702:132479-132733 [Agrobacterium fabacearum]
ATGGCGACGATGAATGTATCCCTGCCAGACCCCATGAAAGATTGGGTTGAAGCACAGGCCAAGACTGGTCGATACTCGAA
TGCGAGCGATTATGTCCGGGACCTGATCCGCAGAGACCAAGCGCGTACGGACAAGATTGCCGAGATGCAGCGATTTGTCG
ACGACGGGATCAGAAGCGGAGTTGGTAGCCGTTCAACGGAAGAGTTGTTTGCTTTAGCCACTTCTCGAGCTGACATCAGC
CGCGGACGCGCTTAA

Structures

Toxin

• AlphaFold DB: A0A4P7TPK7

Antitoxin

• AlphaFold DB: A0A4P7TR46