Detailed information of TA system TA000310

Experimentally validated

Overview

TA module

• Type: II
• Classification (family/domain): yefM-yoeB (relBE)/PHD-RelE
• Location: 3342445..3343003
• Replicon: chromosome
• Accession: NC_002947
• Organism: Pseudomonas putida KT2440

Toxin (Protein)

• Gene name: yoeB
• Uniprot ID: Q88IR0
• Locus tag: PP_2939
• Protein ID: 26989658
• Coordinates: 3342448..3342756 (-)
• Length: 103 a.a.

Antitoxin (Protein)

• Gene name: yefM
• Uniprot ID: Q88IQ9
• Locus tag: PP_2940
• Protein ID: 26989659
• Coordinates: 3342722..3343006 (-)
• Length: 95 a.a.

Genomic Context

Locus tag	Coordinates	Strand	Size (bp)	Protein ID	Product	Description
PP_RS15215 (PP_2935)	3337805..3338998	-	1194	WP_010953835.1	MFS transporter	-
PP_RS15220 (PP_2936)	3339241..3340827	-	1587	WP_010953836.1	ABC-F family ATPase	-
PP_RS15225 (PP_2937)	3340860..3341279	-	420	WP_010953837.1	integrase	-
PP_RS15230 (PP_2938)	3341455..3341928	-	474	WP_049586314.1	OsmC family protein	-
PP_RS15235 (PP_2939)	3342448..3342756	-	309	WP_049586152.1	Txe/YoeB family addiction module toxin	Toxin
PP_RS15240 (PP_2940)	3342722..3343006	-	285	WP_010953840.1	type II toxin-antitoxin system prevent-host-death family antitoxin	Antitoxin
PP_RS15245 (PP_5541)	3343598..3343927	+	330	WP_061405633.1	hypothetical protein	-
PP_RS15250 (PP_5542)	3344014..3344271	+	258	WP_020189883.1	hypothetical protein	-
PP_RS15255 (PP_2941)	3344343..3345008	-	666	WP_049586149.1	SOS response-associated peptidase family protein	-
PP_RS15260 (PP_2942)	3345129..3346499	-	1371	WP_010953842.1	response regulator	-
PP_RS15265 (PP_2943)	3346698..3347696	+	999	WP_010953843.1	cytochrome b6	-

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 (21-100)

Antitoxin

• Type II toxin-antitoxin system, antitoxin Phd/YefM (1-72)

Sequences

Toxin

Protein

• Length: 103 a.a.
• Molecular weight: 12061.78 Da
• Isoelectric Point: 9.1477

>T310 26989658 NC_002947:c3342756-3342448 [Pseudomonas putida KT2440]
MSKNQKQRNKNEARDKVSVKFTKEGWEDYCHWQNADLTILGNINRLIDVCLRTPFTGIGKPEPLKGDLSGLWSRRITREH
RLVYFFEAGMLTVLQCRYHYDD

Nucleotide

• Length: 309 bp

>T310 NC_002947:c3342756-3342448 [Pseudomonas putida KT2440]
ATGAGCAAGAACCAGAAGCAGCGGAACAAGAATGAAGCCCGCGACAAGGTAAGCGTGAAGTTCACCAAGGAGGGCTGGGA
GGATTACTGTCACTGGCAGAATGCCGACCTCACCATCCTCGGCAACATCAACCGCCTAATTGACGTGTGCCTACGCACCC
CCTTCACGGGTATTGGCAAGCCTGAGCCGCTGAAAGGCGATTTATCTGGCTTGTGGTCCCGCCGCATCACCCGTGAGCAC
CGCCTGGTCTACTTCTTCGAGGCCGGTATGCTCACCGTTCTGCAATGCCGCTACCACTACGACGACTAA

Antitoxin

Protein

• Length: 95 a.a.
• Molecular weight: 10610.86 Da
• Isoelectric Point: 4.5562

>AT310 26989659 NC_002947:c3343006-3342722 [Pseudomonas putida KT2440]
MHVLTFSQARAELKQTMDDVCRDHEPAVITRQRGEPVVMMSLEDYNGMNETIHLLGSSKNASRLRSSIAQLRDGQALTKE
LDLNEQEPEAAEQE

Nucleotide

• Length: 285 bp

>AT310 NC_002947:c3343006-3342722 [Pseudomonas putida KT2440]
ATGCACGTACTGACTTTTAGCCAGGCTCGCGCCGAACTGAAGCAGACAATGGATGATGTTTGCCGGGACCATGAGCCCGC
CGTAATCACGCGACAGCGTGGCGAACCCGTAGTGATGATGTCTCTGGAGGACTACAACGGGATGAACGAGACCATTCACC
TGTTGGGATCGTCCAAAAACGCTTCGCGCTTGCGCTCATCCATCGCTCAGCTCCGGGACGGCCAGGCCTTGACGAAGGAA
CTGGACCTCAATGAGCAAGAACCAGAAGCAGCGGAACAAGAATGA

Similar Proteins

Only experimentally validated proteins are listed.

Toxin

Protein	Organism	Identities (%)	Coverage (%)	Ha-value
T6122	Streptomyces coelicolor A3(2)	57.143	100	0.571
T1043	Escherichia coli str. K-12 substr. MG1655	54.762	100	0.548
T130	Mycobacterium tuberculosis H37Rv	54.217	97.647	0.529
T4918	Actinobacillus pleuropneumoniae serovar 3 str. JL03	52.941	98.837	0.523
T728	Streptococcus pneumoniae R6	52.439	97.619	0.512
T10077	Agrobacterium tumefaciens str. C58	52.381	94.382	0.494
T6281	Streptococcus suis SC84	48.81	98.824	0.482
T10182	Aggregatibacter actinomycetemcomitans D11S 1	49.383	97.59	0.482
T6022	Enterococcus faecium	45.679	95.294	0.435
T6115	Enterococcus faecium	45.679	95.294	0.435
T6138	Lactobacillus rhamnosus Lc 705	43.21	94.186	0.407
T10021	Lacticaseibacillus rhamnosus 51B	43.21	94.186	0.407
T10020	Lacticaseibacillus rhamnosus strain 24	43.21	94.186	0.407
T6237	Lactobacillus rhamnosus Lc 705	43.21	94.186	0.407
T6143	Lactobacillus rhamnosus ATCC 8530	43.21	94.186	0.407
T613	Staphylococcus aureus subsp. aureus MW2	39.535	97.727	0.386
T2427	Staphylococcus aureus subsp. aureus NCTC 8325	39.535	97.727	0.386
T1074	Staphylococcus aureus subsp. aureus N315	38.372	97.727	0.375
T10072	Edwardsiella tarda EIB202	39.535	94.505	0.374

Multiple sequence alignment

Antitoxin

Protein	Organism	Identities (%)	Coverage (%)	Ha-value
AT10182	Aggregatibacter actinomycetemcomitans D11S 1	54.878	97.619	0.536
AT1043	Escherichia coli str. K-12 substr. MG1655	45.679	97.59	0.446
AT4918	Actinobacillus pleuropneumoniae serovar 3 str. JL03	44.444	97.59	0.434
AT1074	Staphylococcus aureus subsp. aureus N315	38.554	100	0.386
AT2427	Staphylococcus aureus subsp. aureus NCTC 8325	38.554	100	0.386
AT613	Staphylococcus aureus subsp. aureus MW2	38.554	100	0.386
AT6122	Streptomyces coelicolor A3(2)	42.308	89.655	0.379
AT10072	Edwardsiella tarda EIB202	38.462	96.296	0.37
AT130	Mycobacterium tuberculosis H37Rv	38.75	87.912	0.341
AT10077	Agrobacterium tumefaciens str. C58	36	89.286	0.321
AT6138	Lactobacillus rhamnosus Lc 705	32.927	92.135	0.303
AT6143	Lactobacillus rhamnosus ATCC 8530	32.927	92.135	0.303
AT10020	Lacticaseibacillus rhamnosus strain 24	32.927	92.135	0.303
AT10021	Lacticaseibacillus rhamnosus 51B	32.927	92.135	0.303
AT6237	Lactobacillus rhamnosus Lc 705	32.927	92.135	0.303

Multiple sequence alignment

Structures

Toxin

• AlphaFold DB: Q88IR0

Antitoxin

• AlphaFold DB: Q88IQ9

References

(1) Sirli Rosendahl et al. (2020) Chromosomal toxin-antitoxin systems in Pseudomonas putida are rather selfish than beneficial. Scientific Reports 10(1):9230. [PubMed:32513960]


 experimental literature