Detailed information of TA system TA161579

Bioinformatically predicted

Overview

TA module

• Type: II
• Classification (family/domain): yefM-yoeB (relBE)/YoeB-YefM
• Location: 99897..100399
• Replicon: chromosome
• Accession: NZ_CP055113
• Organism: Shigella flexneri strain SWHIN_101

Toxin (Protein)

• Gene name: yoeB
• Uniprot ID: U9YDH0
• Locus tag: HUZ81_RS00490
• Protein ID: WP_000767829.1
• Coordinates: 100145..100399 (+)
• Length: 85 a.a.

Antitoxin (Protein)

• Gene name: yefM
• Uniprot ID: S1Q063
• Locus tag: HUZ81_RS00485
• Protein ID: WP_001259255.1
• Coordinates: 99897..100148 (+)
• Length: 84 a.a.

Genomic Context

Locus tag	Coordinates	Strand	Size (bp)	Protein ID	Product	Description
HUZ81_RS00460 (95076)	95076..96143	-	1068	WP_000080093.1	bifunctional histidinol-phosphatase/imidazoleglycerol-phosphate dehydratase HisB	-
HUZ81_RS00465 (96143)	96143..97213	-	1071	WP_001468894.1	histidinol-phosphate transaminase	-
HUZ81_RS00470 (97210)	97210..98514	-	1305	WP_021547561.1	histidinol dehydrogenase	-
HUZ81_RS00475 (98520)	98520..99419	-	900	WP_000131782.1	ATP phosphoribosyltransferase	-
HUZ81_RS00480 (99565)	99565..99615	-	51	WP_001364200.1	his operon leader peptide	-
HUZ81_RS00485 (99897)	99897..100148	+	252	WP_001259255.1	YoeB-YefM toxin-antitoxin system antitoxin YefM	Antitoxin
HUZ81_RS00490 (100145)	100145..100399	+	255	WP_000767829.1	type II toxin-antitoxin system mRNA interferase toxin YoeB	Toxin
HUZ81_RS00495 (100482)	100482..101306	+	825	WP_000754737.1	SDR family oxidoreductase	-
HUZ81_RS00500 (101352)	101352..102281	+	930	WP_000803360.1	LysR substrate-binding domain-containing protein	-
HUZ81_RS00505 (102496)	102496..102558	+	63	WP_010723108.1	membrane protein YoeI	-
HUZ81_RS00510 (102548)	102548..103906	+	1359	WP_000019197.1	putrescine/proton symporter PlaP	-
HUZ81_RS00515 (104085)	104085..105143	+	1059	WP_000492340.1	thiosulfate utilization transporter TsuA/YeeE	-
HUZ81_RS00520 (105157)	105157..105384	+	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

>T161579 WP_000767829.1 NZ_CP055113:100145-100399 [Shigella flexneri]
VKLIWSEESWDDYLYWQETDKRIVKKINELIKDTRRTPFEGKGKPEPLKHNLSGFWSRRITEEHRLVYAVTDDSLLIAAC
RYHY

Nucleotide

• Length: 255 bp

>T161579 NZ_CP071224:55329-55604 [Serratia marcescens subsp. marcescens ATCC 13880]
ATGGAATTAAAATGGACGAGTAAGGCGCTATCGGATTTGGCGCGTTTGTTTGAGTTTCTTGCCTTGGCTAACCGCACTGC
GGCAGCGAATTCGGTGAAGGCCTTGGTCGCCGCGCCTAAAGCGTTGCTCGATAATCCTCGCCTGGGTGAAAGACTGGATG
AGTTTTTACCGCAGGAAGTGAGGCGTATTCTGGTCGGCCGTTATGAGATACGTTACCAGGTGCAGCCGGCAACGATTTAT
GTTCTGCGTATTTGGCATACCCGCGAAGAGCGATAG

Antitoxin

Protein

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

>AT161579 WP_001259255.1 NZ_CP055113:99897-100148 [Shigella flexneri]
MRTISYSEARQNLSATMMKAVEDHAPILITRQNGEACVLMSLEEYNSLEETAYLLRSPANARRLMDSIDSLKSGKGTEKD
IIE

Nucleotide

• Length: 252 bp

>AT161579 NZ_CP071224:55069-55329 [Serratia marcescens subsp. marcescens ATCC 13880]
ATGAATACGAAAGTCATCACCGCTCATGTGCCGCTGCCTTTGGCTGAAAAGGTGGATGAAATGGCCGCCAAACTTGAACG
TTCACGGGGATGGATAGTGAAGCAAGCCCTCGCCGCCTGGCTTGAGCAAGAGGAAGAACGCCGTCGATTAACGCTGGCGG
CGCTGGCCGATGTCGAACAGCAAAACGTTATCGATCATGAGTCGGTAGAAGCCTGGGCTGCCAGCCTGGACAGTGACGAG
CCGCTGCCGGTACCGCGCTGA

Structures

Toxin

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

Antitoxin

• PDB: 2A6Q
• AlphaFold DB: A0A7U9LNR0