Detailed information of TA system TA000728

Experimentally validated

Overview

TA module

• Type: II
• Classification (family/domain): yefM-yoeB (relBE)/PHD-RelE
• Location: 1566450..1567001
• Replicon: chromosome
• Accession: NC_003098
• Organism: Streptococcus pneumoniae R6

Toxin (Protein)

• Gene name: yoeB
• Uniprot ID: Q8DNR3
• Locus tag: spr1585
• Protein ID: 15903627
• Coordinates: 1566450..1566704 (-)
• Length: 85 a.a.

Antitoxin (Protein)

• Gene name: yefM
• Uniprot ID: Q8DNR2
• Locus tag: spr1586
• Protein ID: 15903628
• Coordinates: 1566708..1566962 (-)
• Length: 85 a.a.

Genomic Context

Locus tag	Coordinates	Strand	Size (bp)	Protein ID	Product	Description
SPR_RS07845 (spr1582)	1563551..1563865	-	315	WP_000979235.1	DNA-directed RNA polymerase subunit omega	-
SPR_RS07850 (spr1583)	1563890..1564516	-	627	WP_000775044.1	guanylate kinase	-
SPR_RS07855 (spr1584)	1564646..1566259	-	1614	WP_000404940.1	ribonuclease Y	-
SPR_RS07860 (spr1585)	1566450..1566704	-	255	WP_000924721.1	Txe/YoeB family addiction module toxin	Toxin
SPR_RS07865 (spr1586)	1566708..1566962	-	255	WP_000388572.1	type II toxin-antitoxin system Phd/YefM family antitoxin	Antitoxin
SPR_RS07870 (spr1587)	1567200..1568297	-	1098	WP_000156355.1	nucleotidyltransferase	-
SPR_RS07875 (spr1588)	1568307..1569053	-	747	WP_000605157.1	class I SAM-dependent methyltransferase	-
SPR_RS07880 (spr1589)	1569156..1569509	-	354	WP_001003001.1	ribosome silencing factor	-
SPR_RS07885 (spr1590)	1569522..1570022	-	501	WP_000844717.1	cysteine hydrolase	-
SPR_RS07890 (spr1591)	1570023..1570616	-	594	WP_000121655.1	bis(5'-nucleosyl)-tetraphosphatase (symmetrical) YqeK	-
SPR_RS07895 (spr1592)	1570616..1571245	-	630	WP_000151313.1	nicotinate-nucleotide adenylyltransferase	-
SPR_RS07900 (spr1593)	1571297..1571608	-	312	WP_000060169.1	ribosome assembly RNA-binding protein YhbY	-

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 (1-84)

Antitoxin

• Type II toxin-antitoxin system, antitoxin Phd/YefM (1-75)

Sequences

Toxin

Protein

• Length: 85 a.a.
• Molecular weight: 10115.55 Da
• Isoelectric Point: 7.9716

>T728 15903627 NC_003098:c1566704-1566450 [Streptococcus pneumoniae R6]
MLLKFTEDAWADYCYWQNQDKKTLKRINKLIKDIQRDPFTGIGKPEPLKYDYQGAWSRRIDAENRLIYMMDGDSVAFLSF
KDHY

Nucleotide

• Length: 255 bp

>T728 NC_003098:c1566704-1566450 [Streptococcus pneumoniae R6]
ATGCTACTCAAGTTTACAGAAGATGCCTGGGCAGATTATTGCTACTGGCAAAACCAAGATAAAAAAACACTAAAAAGAAT
CAATAAATTAATCAAGGATATTCAACGCGATCCATTTACAGGAATAGGAAAACCAGAGCCACTCAAATATGATTACCAAG
GAGCCTGGTCACGGCGTATTGATGCAGAAAATCGCTTGATTTATATGATGGATGGAGATAGCGTGGCTTTCTTGTCCTTT
AAAGATCATTACTAA

Antitoxin

Protein

• Length: 85 a.a.
• Molecular weight: 9706.00 Da
• Isoelectric Point: 4.8430

>AT728 15903628 NC_003098:c1566962-1566708 [Streptococcus pneumoniae R6]
MEAVLYSTFRNHLKDYMKKVNDEFEPLTVVNKNPDEDIVVLSKSEWDSIQETLRIAQNKELSDKVLRGMAQVRAGSTQVH
VIEE

Nucleotide

• Length: 255 bp

>AT728 NC_003098:c1566962-1566708 [Streptococcus pneumoniae R6]
ATGGAAGCAGTCCTTTACTCAACATTCCGAAATCATTTAAAGGACTACATGAAGAAGGTAAATGATGAATTTGAGCCTTT
GACGGTGGTCAATAAAAATCCAGATGAGGACATTGTAGTTCTTTCAAAGAGCGAATGGGACAGTATTCAGGAAACCCTGA
GAATCGCCCAAAATAAGGAGTTATCAGACAAGGTTTTACGAGGAATGGCTCAAGTCCGTGCTGGAAGCACTCAGGTCCAT
GTGATTGAGGAGTGA

Similar Proteins

Only experimentally validated proteins are listed.

Toxin

Protein	Organism	Identities (%)	Coverage (%)	Ha-value
T6281	Streptococcus suis SC84	75	100	0.75
T6115	Enterococcus faecium	55.294	100	0.56
T10021	Lacticaseibacillus rhamnosus 51B	55.294	100	0.56
T10020	Lacticaseibacillus rhamnosus strain 24	55.294	100	0.56
T6237	Lactobacillus rhamnosus Lc 705	55.294	100	0.56
T6022	Enterococcus faecium	55.294	100	0.56
T6138	Lactobacillus rhamnosus Lc 705	55.294	100	0.56
T6143	Lactobacillus rhamnosus ATCC 8530	55.294	100	0.56
T4918	Actinobacillus pleuropneumoniae serovar 3 str. JL03	55.952	100	0.56
T310	Pseudomonas putida KT2440	52.439	97.619	0.512
T130	Mycobacterium tuberculosis H37Rv	52.439	97.619	0.512
T1043	Escherichia coli str. K-12 substr. MG1655	51.22	97.619	0.5
T6122	Streptomyces coelicolor A3(2)	51.22	97.619	0.5
T2427	Staphylococcus aureus subsp. aureus NCTC 8325	45.783	98.81	0.452
T613	Staphylococcus aureus subsp. aureus MW2	45.783	98.81	0.452
T1074	Staphylococcus aureus subsp. aureus N315	44.578	98.81	0.44
T10077	Agrobacterium tumefaciens str. C58	48.649	88.095	0.429
T10072	Edwardsiella tarda EIB202	40.964	98.81	0.405

Multiple sequence alignment

Antitoxin

Protein	Organism	Identities (%)	Coverage (%)	Ha-value
AT6281	Streptococcus suis SC84	79.487	92.857	0.738
AT10182	Aggregatibacter actinomycetemcomitans D11S 1	54.762	100	0.548
AT6138	Lactobacillus rhamnosus Lc 705	47.5	95.238	0.452
AT6143	Lactobacillus rhamnosus ATCC 8530	47.5	95.238	0.452
AT6237	Lactobacillus rhamnosus Lc 705	47.5	95.238	0.452
AT10020	Lacticaseibacillus rhamnosus strain 24	47.5	95.238	0.452
AT10021	Lacticaseibacillus rhamnosus 51B	47.5	95.238	0.452
AT6115	Enterococcus faecium	46.25	95.238	0.44
AT6022	Enterococcus faecium	46.25	95.238	0.44
AT613	Staphylococcus aureus subsp. aureus MW2	34.722	86.747	0.301
AT1074	Staphylococcus aureus subsp. aureus N315	34.722	86.747	0.301
AT2427	Staphylococcus aureus subsp. aureus NCTC 8325	34.722	86.747	0.301

Multiple sequence alignment

Structures

Toxin

• AlphaFold DB: Q8DNR3

Antitoxin

• AlphaFold DB: Q8DNR2

References

(1) Wai Ting Chan et al. (2018) The Streptococcus pneumoniaeyefM-yoeB and relBE Toxin-Antitoxin Operons Participate in Oxidative Stress and Biofilm Formation. Toxins 10(9):378. [PubMed:30231554]


 experimental literature