Detailed information of TA system TA161859

Bioinformatically predicted

Overview

TA module

• Type: II
• Classification (family/domain): yefM-yoeB (relBE)/YoeB-YefM
• Location: 1843107..1843609
• Replicon: chromosome
• Accession: NZ_CP055194
• Organism: Shigella flexneri strain STEFF_10

Toxin (Protein)

• Gene name: yoeB
• Uniprot ID: U9YDH0
• Locus tag: HUZ40_RS08865
• Protein ID: WP_000767829.1
• Coordinates: 1843355..1843609 (+)
• Length: 85 a.a.

Antitoxin (Protein)

• Gene name: yefM
• Uniprot ID: S1Q063
• Locus tag: HUZ40_RS08860
• Protein ID: WP_001259255.1
• Coordinates: 1843107..1843358 (+)
• Length: 84 a.a.

Genomic Context

Locus tag	Coordinates	Strand	Size (bp)	Protein ID	Product	Description
HUZ40_RS08835 (1838285)	1838285..1839352	-	1068	WP_000080067.1	bifunctional histidinol-phosphatase/imidazoleglycerol-phosphate dehydratase HisB	-
HUZ40_RS08840 (1839352)	1839352..1840422	-	1071	WP_203152312.1	histidinol-phosphate transaminase	-
HUZ40_RS08845 (1840419)	1840419..1841723	-	1305	WP_001295420.1	histidinol dehydrogenase	-
HUZ40_RS08850 (1841729)	1841729..1842628	-	900	WP_000131782.1	ATP phosphoribosyltransferase	-
HUZ40_RS08855 (1842774)	1842774..1842824	-	51	WP_001364200.1	his operon leader peptide	-
HUZ40_RS08860 (1843107)	1843107..1843358	+	252	WP_001259255.1	YoeB-YefM toxin-antitoxin system antitoxin YefM	Antitoxin
HUZ40_RS08865 (1843355)	1843355..1843609	+	255	WP_000767829.1	type II toxin-antitoxin system mRNA interferase toxin YoeB	Toxin
HUZ40_RS08870 (1843692)	1843692..1844516	+	825	WP_000754737.1	SDR family oxidoreductase	-
HUZ40_RS08875 (1844562)	1844562..1845491	+	930	WP_000803351.1	LysR substrate-binding domain-containing protein	-
HUZ40_RS08880 (1845706)	1845706..1845768	+	63	WP_010723108.1	membrane protein YoeI	-
HUZ40_RS08885 (1845758)	1845758..1847116	+	1359	WP_000019197.1	putrescine/proton symporter PlaP	-
HUZ40_RS08890 (1847295)	1847295..1848353	+	1059	WP_000492325.1	thiosulfate utilization transporter TsuA/YeeE	-
HUZ40_RS08895 (1848367)	1848367..1848594	+	228	WP_000985273.1	thiosulfate utilization sulfurtransferase TsuB/YeeD	-

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

>T161859 WP_000767829.1 NZ_CP055194:1843355-1843609 [Shigella flexneri]
VKLIWSEESWDDYLYWQETDKRIVKKINELIKDTRRTPFEGKGKPEPLKHNLSGFWSRRITEEHRLVYAVTDDSLLIAAC
RYHY

Nucleotide

• Length: 255 bp

>T161859 NZ_CP071382:c629172-628894 [Geobacter sp. Jerry-YX]
ATGATCAAGACCTTCCGCTGCAAGGACACCCAGGCATTGTTCGAGGGCAAAAGCCCGCGCCGCTTCAAGGCGTTCGCTAC
GGTTGCCGAGCGAAAGCTGCAAATGCTCGACGATGCCCATGCGCCCGAAGATCTCCGATCCCCGCCGGGCAACCGTCTGG
AAGCCCTGCGCGGCGACCGCAAAGGACAGTGGAGTATCCGAATCAACGATCAGTGGCGCCTCTGTTTTCGCCTCGAGGAT
GGCAACGCCTTTGATGTCGAGATCGTGGATTACCATTGA

Antitoxin

Protein

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

>AT161859 WP_001259255.1 NZ_CP055194:1843107-1843358 [Shigella flexneri]
MRTISYSEARQNLSATMMKAVEDHAPILITRQNGEACVLMSLEEYNSLEETAYLLRSPANARRLMDSIDSLKSGKGTEKD
IIE

Nucleotide

• Length: 252 bp

>AT161859 NZ_CP071382:c628880-628575 [Geobacter sp. Jerry-YX]
ATGAATCCCACAAACAGAATGCGCCCCATCCATCCCGGTGAAGTGTTGCGAGAAGAATTTCTTGTTCCCTTGGGGATGAG
CGCCCATGCGCTGGCGCTTGAACTCAAGGTGCCTGCCCCGCGCATCAACGACATCGTGCGCGAGCGCCGTGCCGTCACGC
CGGATACGGCACTAAGGCTGGCCCGGTACTTCGGCACGACTCCCCAGTTCTGGCTTAATCTTCAGACCAGCTATGACCTT
AAGATCGCCGAACGGGAGCTGGGGACGAAAATTGAGCGTGAAGTCCATACTCGCCTAGTGGCGTAA

Structures

Toxin

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

Antitoxin

• AlphaFold DB: A0A7U9LNR0