Detailed information of TA system TA111950

Bioinformatically predicted

Overview

TA module

• Type: II
• Classification (family/domain): yefM-yoeB (relBE)/YoeB-YefM
• Location: 4465679..4466181
• Replicon: chromosome
• Accession: NZ_CP032523
• Organism: Shigella sonnei strain AR_0030

Toxin (Protein)

• Gene name: yoeB
• Uniprot ID: U9YDH0
• Locus tag: AM357_RS23275
• Protein ID: WP_000767829.1
• Coordinates: 4465679..4465933 (-)
• Length: 85 a.a.

Antitoxin (Protein)

• Gene name: yefM
• Uniprot ID: S1Q063
• Locus tag: AM357_RS23280
• Protein ID: WP_001259255.1
• Coordinates: 4465930..4466181 (-)
• Length: 84 a.a.

Genomic Context

Locus tag	Coordinates	Strand	Size (bp)	Protein ID	Product	Description
AM357_RS23245 (4460694)	4460694..4460921	-	228	WP_000985273.1	thiosulfate utilization sulfurtransferase TsuB/YeeD	-
AM357_RS23250 (4460935)	4460935..4461993	-	1059	WP_000492295.1	thiosulfate utilization transporter TsuA/YeeE	-
AM357_RS23255 (4462172)	4462172..4463530	-	1359	WP_000019197.1	putrescine/proton symporter PlaP	-
AM357_RS23260 (4463520)	4463520..4463582	-	63	WP_010723108.1	membrane protein YoeI	-
AM357_RS23265 (4463797)	4463797..4464726	-	930	WP_005149930.1	LysR substrate-binding domain-containing protein	-
AM357_RS23270 (4464772)	4464772..4465596	-	825	WP_000754737.1	SDR family oxidoreductase	-
AM357_RS23275 (4465679)	4465679..4465933	-	255	WP_000767829.1	type II toxin-antitoxin system mRNA interferase toxin YoeB	Toxin
AM357_RS23280 (4465930)	4465930..4466181	-	252	WP_001259255.1	YoeB-YefM toxin-antitoxin system antitoxin YefM	Antitoxin
AM357_RS23285 (4466464)	4466464..4466514	+	51	WP_001364200.1	his operon leader peptide	-
AM357_RS23290 (4466660)	4466660..4467559	+	900	WP_000131782.1	ATP phosphoribosyltransferase	-
AM357_RS23295 (4467565)	4467565..4468869	+	1305	WP_001462576.1	histidinol dehydrogenase	-
AM357_RS23300 (4468866)	4468866..4469936	+	1071	WP_000108977.1	histidinol-phosphate transaminase	-
AM357_RS23305 (4469936)	4469936..4471003	+	1068	WP_000080086.1	bifunctional histidinol-phosphatase/imidazoleglycerol-phosphate dehydratase HisB	-

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

• Toxin YoeB (2-84)

Antitoxin

• Type II toxin-antitoxin system, antitoxin Phd/YefM (1-73)

Sequences

Toxin

Protein

• Length: 85 a.a.
• Molecular weight: 10183.58 Da
• Isoelectric Point: 8.0353

>T111950 WP_000767829.1 NZ_CP032523:c4465933-4465679 [Shigella sonnei]
VKLIWSEESWDDYLYWQETDKRIVKKINELIKDTRRTPFEGKGKPEPLKHNLSGFWSRRITEEHRLVYAVTDDSLLIAAC
RYHY

Nucleotide

• Length: 255 bp

>T111950 NZ_CP032523:c4465933-4465679 [Shigella sonnei]
GTGAAACTAATCTGGTCTGAGGAATCATGGGATGATTATCTGTACTGGCAGGAAACAGATAAGCGAATTGTTAAAAAGAT
CAATGAACTTATCAAAGATACCCGCAGAACGCCATTTGAAGGTAAGGGGAAGCCAGAACCCCTGAAACATAATTTGTCAG
GTTTCTGGTCCCGACGCATTACAGAGGAGCACCGTCTGGTATACGCGGTTACCGACGATTCACTGCTCATTGCAGCATGT
CGTTATCATTATTGA

Antitoxin

Protein

• Length: 84 a.a.
• Molecular weight: 9307.58 Da
• Isoelectric Point: 4.7954

>AT111950 WP_001259255.1 NZ_CP032523:c4466181-4465930 [Shigella sonnei]
MRTISYSEARQNLSATMMKAVEDHAPILITRQNGEACVLMSLEEYNSLEETAYLLRSPANARRLMDSIDSLKSGKGTEKD
IIE

Nucleotide

• Length: 252 bp

>AT111950 NZ_CP032523:c4466181-4465930 [Shigella sonnei]
ATGCGTACAATTAGCTACAGCGAAGCGCGTCAGAATTTGTCGGCAACAATGATGAAAGCCGTTGAAGATCATGCCCCGAT
CCTTATTACTCGTCAGAATGGAGAGGCTTGTGTTCTGATGTCACTCGAAGAATACAACTCGCTGGAAGAGACGGCTTATC
TACTGCGCTCCCCCGCTAACGCCCGGAGATTGATGGACTCAATCGATAGCCTGAAATCAGGCAAAGGAACAGAAAAGGAC
ATTATTGAGTGA

Structures

Toxin

• PDB: 6NY6
• PDB: 2A6S
• PDB: 6OXA
• PDB: 2A6R
• PDB: 4V8X
• PDB: 6OTR
• PDB: 6OXI
• PDB: 2A6Q

Antitoxin

• AlphaFold DB: A0A7U9LNR0