Detailed information of TA system TA079066

Bioinformatically predicted

Overview

TA module

• Type: II
• Classification (family/domain): yefM-yoeB (relBE)/YoeB-YefM
• Location: 1183485..1183987
• Replicon: chromosome
• Accession: NZ_CP022455
• Organism: Shigella sonnei strain 2015C-3794

Toxin (Protein)

• Gene name: yoeB
• Uniprot ID: U9YDH0
• Locus tag: B9129_RS07005
• Protein ID: WP_000767829.1
• Coordinates: 1183485..1183739 (-)
• Length: 85 a.a.

Antitoxin (Protein)

• Gene name: yefM
• Uniprot ID: S1Q063
• Locus tag: B9129_RS07010
• Protein ID: WP_001259255.1
• Coordinates: 1183736..1183987 (-)
• Length: 84 a.a.

Genomic Context

Locus tag	Coordinates	Strand	Size (bp)	Protein ID	Product	Description
B9129_RS06980 (1178501)	1178501..1178728	-	228	WP_000985273.1	thiosulfate utilization sulfurtransferase TsuB/YeeD	-
B9129_RS06985 (1178742)	1178742..1179800	-	1059	WP_000492295.1	thiosulfate utilization transporter TsuA/YeeE	-
B9129_RS06990 (1179979)	1179979..1181337	-	1359	WP_000019197.1	putrescine/proton symporter PlaP	-
B9129_RS27095 (1181327)	1181327..1181389	-	63	WP_010723108.1	membrane protein YoeI	-
B9129_RS06995 (1181603)	1181603..1182532	-	930	WP_000811606.1	LysR substrate-binding domain-containing protein	-
B9129_RS07000 (1182578)	1182578..1183402	-	825	WP_000754737.1	SDR family oxidoreductase	-
B9129_RS07005 (1183485)	1183485..1183739	-	255	WP_000767829.1	type II toxin-antitoxin system mRNA interferase toxin YoeB	Toxin
B9129_RS07010 (1183736)	1183736..1183987	-	252	WP_001259255.1	YoeB-YefM toxin-antitoxin system antitoxin YefM	Antitoxin
B9129_RS07015 (1184270)	1184270..1184320	+	51	WP_001364200.1	his operon leader peptide	-
B9129_RS07025 (1184466)	1184466..1185365	+	900	WP_000131782.1	ATP phosphoribosyltransferase	-
B9129_RS07030 (1185371)	1185371..1186675	+	1305	WP_001462576.1	histidinol dehydrogenase	-
B9129_RS07035 (1186672)	1186672..1187742	+	1071	WP_039063509.1	histidinol-phosphate transaminase	-
B9129_RS07040 (1187742)	1187742..1188809	+	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

>T79066 WP_000767829.1 NZ_CP022455:c1183739-1183485 [Shigella sonnei]
VKLIWSEESWDDYLYWQETDKRIVKKINELIKDTRRTPFEGKGKPEPLKHNLSGFWSRRITEEHRLVYAVTDDSLLIAAC
RYHY

Nucleotide

• Length: 255 bp

>T79066 NZ_CP022455:c1183739-1183485 [Shigella sonnei]
GTGAAACTAATCTGGTCTGAGGAATCATGGGATGATTATCTGTACTGGCAGGAAACAGATAAGCGAATTGTTAAAAAGAT
CAATGAACTTATCAAAGATACCCGCAGAACGCCATTTGAAGGTAAGGGGAAGCCAGAACCCCTGAAACATAATTTGTCAG
GTTTCTGGTCCCGACGCATTACAGAGGAGCACCGTCTGGTATACGCGGTTACCGACGATTCACTGCTCATTGCAGCATGT
CGTTATCATTATTGA

Antitoxin

Protein

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

>AT79066 WP_001259255.1 NZ_CP022455:c1183987-1183736 [Shigella sonnei]
MRTISYSEARQNLSATMMKAVEDHAPILITRQNGEACVLMSLEEYNSLEETAYLLRSPANARRLMDSIDSLKSGKGTEKD
IIE

Nucleotide

• Length: 252 bp

>AT79066 NZ_CP022455:c1183987-1183736 [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