Detailed information of TA system TA006290

Experimentally validated

Overview

TA module

• Type: II
• Classification (family/domain): DinJ-YafQ (relBE)/-
• Location: 242448..242989
• Replicon: chromosome
• Accession: NZ_CP009273
• Organism: Escherichia coli BW25113

Toxin (Protein)

• Gene name: yafQ
• Uniprot ID: Q47149
• Locus tag: BW25113_RS01140
• Protein ID: WP_000615983.1
• Coordinates: 242448..242726 (-)
• Length: 93 a.a.

Antitoxin (Protein)

• Gene name: dinJ
• Uniprot ID: Q47150
• Locus tag: BW25113_RS01145
• Protein ID: WP_000729703.1
• Coordinates: 242729..242989 (-)
• Length: 87 a.a.

Genomic Context

Locus tag	Coordinates	Strand	Size (bp)	Protein ID	Product	Description
BW25113_RS01125 (BW25113_0222)	240030..240608	+	579	WP_000284050.1	D-sedoheptulose 7-phosphate isomerase	-
BW25113_RS01130 (BW25113_0223)	240814..241581	+	768	WP_000333380.1	class II glutamine amidotransferase	-
BW25113_RS01135 (BW25113_0224)	241552..242292	-	741	WP_001225679.1	murein L,D-transpeptidase	-
BW25113_RS01140 (BW25113_0225)	242448..242726	-	279	WP_000615983.1	type II toxin-antitoxin system mRNA interferase toxin YafQ	Toxin
BW25113_RS01145 (BW25113_0226)	242729..242989	-	261	WP_000729703.1	type II toxin-antitoxin system antitoxin DinJ	Antitoxin
BW25113_RS01150 (BW25113_0227)	243199..243948	+	750	WP_000056849.1	C40 family peptidase	-
BW25113_RS01155 (BW25113_0228)	244124..244621	+	498	WP_000006255.1	REP-associated tyrosine transposase RayT	-
BW25113_RS01160 (BW25113_0229)	244845..246557	-	1713	Protein_222	flagellar biosynthesis protein FlhA	-
BW25113_RS01165 (BW25113_0230)	246529..247314	+	786	WP_000207552.1	putative lateral flagellar export/assembly protein LafU	-

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-antitoxin system, YafQ-like toxin (4-91)

Antitoxin

• RelB antitoxin/Antitoxin DinJ (1-85)

Sequences

Toxin

Protein

• Length: 93 a.a.
• Molecular weight: 10846.62 Da
• Isoelectric Point: 9.9941

>T6290 WP_000615983.1 NZ_CP009273:c242726-242448 [Escherichia coli BW25113]
MIQRDIEYSGQYSKDVKLAQKRHKDMNKLKYLMTLLINNTLPLPAVYKDHPLQGSWKGYRDAHVEPDWILIYKLTDKLLR
FERTGTHAALFG

Nucleotide

• Length: 279 bp

>T6290 NZ_CP009273:c242726-242448 [Escherichia coli BW25113]
ATGATTCAAAGGGATATTGAATACTCGGGACAATATTCAAAGGATGTAAAACTTGCACAAAAGCGTCATAAGGATATGAA
TAAATTGAAATATCTTATGACGCTTCTTATCAATAATACTTTACCGCTTCCAGCTGTTTATAAAGACCACCCGCTGCAAG
GTTCATGGAAAGGTTATCGCGATGCTCATGTCGAACCGGACTGGATCCTGATTTACAAACTTACCGATAAACTTTTACGA
TTTGAGAGAACTGGAACTCACGCGGCGCTCTTTGGGTAA

Antitoxin

Protein

• Length: 87 a.a.
• Molecular weight: 9405.80 Da
• Isoelectric Point: 5.0758

>AT6290 WP_000729703.1 NZ_CP009273:c242989-242729 [Escherichia coli BW25113]
MAANAFVRARIDEDLKNQAADVLAGMGLTISDLVRITLTKVAREKALPFDLREPNQLTIQSIKNSEAGIDVHKAKDADDL
FDKLGI

Nucleotide

• Length: 261 bp

>AT6290 NZ_CP009273:c242989-242729 [Escherichia coli BW25113]
ATGGCTGCTAACGCGTTTGTTCGCGCCCGAATCGATGAAGATCTGAAGAATCAGGCAGCGGACGTACTGGCCGGGATGGG
GCTGACCATCTCTGACCTGGTTCGCATAACCCTCACAAAGGTCGCGCGTGAAAAGGCATTGCCGTTTGATTTACGCGAGC
CTAATCAATTAACCATTCAATCAATCAAAAACAGCGAAGCTGGCATTGATGTTCATAAGGCCAAAGACGCCGATGATTTA
TTTGATAAATTAGGAATTTAA

Similar Proteins

Only experimentally validated proteins are listed.

Toxin

Protein	Organism	Identities (%)	Coverage (%)	Ha-value
T1038	Escherichia coli str. K-12 substr. MG1655	100	100	1
T10190	Pseudomonas sp. strain ANT_J3	45.263	100	0.467
T10111	Lacticaseibacillus paracasei strain 4366 DinJ and YafQ genes	41.111	97.826	0.402
T10112	Lacticaseibacillus paracasei strain 2333 DinJ and YafQ genes	40	97.826	0.391
T10095	Clostridium difficile R20291	40.449	96.739	0.391
T6256	Bifidobacterium longum subsp. infantis ATCC 15697 = JCM 1222	36.17	100	0.37
T6127	Helicobacter pylori 26695	37.5	97.778	0.367
T10136	Pseudomonas savastanoi	38.824	92.391	0.359
T665	Streptococcus mutans UA159	37.079	96.739	0.359
T166	Vibrio cholerae O1 biovar El Tor str. N16961	35.632	97.753	0.348
T10109	Lacticaseibacillus rhamnosus strain 2360 DinJ and YafQ genes	34.118	92.391	0.315
T6139	Lactobacillus rhamnosus Lc 705	42.222	73.77	0.311
T6144	Lactobacillus rhamnosus ATCC 8530	42.222	73.77	0.311
T6239	Lactobacillus rhamnosus ATCC 8530	42.222	73.77	0.311
T10108	Lacticaseibacillus rhamnosus strain 1473 DinJ and YafQ genes	42.222	73.77	0.311
T10110	Lacticaseibacillus rhamnosus strain 1019 DinJ and YafQ genes	42.222	73.77	0.311

Multiple sequence alignment

Antitoxin

Protein	Organism	Identities (%)	Coverage (%)	Ha-value
AT1038	Escherichia coli str. K-12 substr. MG1655	100	100	1
AT10190	Pseudomonas sp. strain ANT_J3	38.961	89.535	0.349
AT6097	Sinorhizobium meliloti 1021	56.863	59.302	0.337
AT10136	Pseudomonas savastanoi	35.366	95.349	0.337
AT10095	Clostridium difficile R20291	29.885	100	0.302

Multiple sequence alignment

Structures

Toxin

• PDB: 4Q2U

Antitoxin

• AlphaFold DB: A0A5F1F716

References

(1) Yoshimitsu Masuda et al. (2020) Role of Toxin-Antitoxin-Regulated Persister Population and Indole in Bacterial Heat Tolerance. Applied And Environmental Microbiology 86(16):e00935-20. [PubMed:32503909]

(2) Yueju Zhao et al. (2016) Toxin YafQ Reduces Escherichia coli Growth at Low Temperatures. PloS One 11(8):e0161577. [PubMed:27557125]


 experimental literature