Detailed information of TA system TA006237

Experimentally validated

Overview

TA module

• Type: II
• Classification (family/domain): yefM-yoeB (relBE)/RelE(toxin)
• Location: 2763807..2764329
• Replicon: chromosome
• Accession: NC_013199
• Organism: Lactobacillus rhamnosus Lc 705

Toxin (Protein)

• Gene name: yoeB
• Uniprot ID: C2JUK2
• Locus tag: LC705_RS12925
• Protein ID: WP_005687756.1
• Coordinates: 2764069..2764329 (+)
• Length: 87 a.a.

Antitoxin (Protein)

• Gene name: yefM
• Uniprot ID: C2JUK3
• Locus tag: LC705_RS12920
• Protein ID: WP_005687754.1
• Coordinates: 2763807..2764076 (+)
• Length: 90 a.a.

Genomic Context

Locus tag	Coordinates	Strand	Size (bp)	Protein ID	Product	Description
LC705_RS12900 (LC705_02722)	2759394..2759963	-	570	WP_005687747.1	PTS glucitol/sorbitol transporter subunit IIC	-
LC705_RS12905 (LC705_02723)	2759976..2760485	-	510	WP_005690780.1	transcriptional regulator GutM	-
LC705_RS12910 (LC705_02724)	2760486..2762354	-	1869	WP_014571687.1	HTH domain-containing protein	-
LC705_RS12915 (LC705_02725)	2762381..2763181	-	801	WP_005690776.1	SDR family oxidoreductase	-
LC705_RS12920 (LC705_02726)	2763807..2764076	+	270	WP_005687754.1	type II toxin-antitoxin system prevent-host-death family antitoxin	Antitoxin
LC705_RS12925 (LC705_02727)	2764069..2764329	+	261	WP_005687756.1	Txe/YoeB family addiction module toxin	Toxin
LC705_RS12930 (LC705_02728)	2764540..2765268	-	729	WP_014571689.1	L-ribulose-5-phosphate 4-epimerase	-
LC705_RS12935 (LC705_02729)	2765465..2766286	+	822	WP_005690770.1	Cof-type HAD-IIB family hydrolase	-
LC705_RS12940 (LC705_02730)	2766353..2767240	-	888	WP_014571690.1	L-ribulose-5-phosphate 3-epimerase	-
LC705_RS12945 (LC705_02731)	2767425..2768204	-	780	WP_173011709.1	DeoR/GlpR family DNA-binding transcription regulator	-
LC705_RS12950 (LC705_02732)	2768272..2768913	-	642	WP_005690763.1	3-keto-L-gulonate-6-phosphate decarboxylase UlaD	-

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 (5-85)

Antitoxin

• Type II toxin-antitoxin system, antitoxin Phd/YefM (1-74)

Sequences

Toxin

Protein

• Length: 87 a.a.
• Molecular weight: 10485.91 Da
• Isoelectric Point: 9.6577

>T6237 WP_005687756.1 NC_013199:2764069-2764329 [Lactobacillus rhamnosus Lc 705]
MIKTWTDDAWADYMYWHDQNDKRTIKRINQLIQAIDRDPYKGIGKPEPLRYALTGKWSRRIDQENRIIYSIEKNHINIFA
CRTHYS

Nucleotide

• Length: 261 bp

>T6237 NC_013199:2764069-2764329 [Lactobacillus rhamnosus Lc 705]
ATGATTAAAACCTGGACCGATGATGCTTGGGCGGACTACATGTATTGGCATGATCAAAACGACAAGCGGACAATCAAACG
AATTAATCAACTCATTCAAGCCATTGACCGTGACCCTTATAAAGGCATCGGAAAACCTGAGCCACTTAGATATGCGCTAA
CCGGAAAATGGTCACGTCGGATTGATCAGGAAAATCGCATCATCTACAGCATTGAAAAGAACCACATTAATATTTTCGCC
TGCCGCACTCACTACAGTTAA

Antitoxin

Protein

• Length: 90 a.a.
• Molecular weight: 10181.39 Da
• Isoelectric Point: 4.6755

>AT6237 WP_005687754.1 NC_013199:2763807-2764076 [Lactobacillus rhamnosus Lc 705]
MEATNYSDFRRNLKHYMSQVNEDAEPLLVTAKDDDDNVVVMSKHDFDAIEETLYLLSNPKLMAKIKRGDAQIAAGKAKQH
ELLTDFDHD

Nucleotide

• Length: 270 bp

>AT6237 NC_013199:2763807-2764076 [Lactobacillus rhamnosus Lc 705]
ATGGAAGCAACGAATTATAGTGATTTCCGCCGCAACCTTAAGCATTATATGAGTCAAGTCAACGAAGACGCCGAACCGCT
ACTGGTTACCGCTAAAGATGATGATGACAATGTGGTGGTTATGAGCAAGCACGATTTTGACGCCATCGAAGAAACCCTGT
ATTTACTCAGCAATCCCAAGCTGATGGCCAAAATCAAACGTGGTGATGCCCAAATTGCCGCTGGAAAGGCTAAACAGCAC
GAGTTGTTAACGGACTTCGATCATGATTAA

Similar Proteins

Only experimentally validated proteins are listed.

Toxin

Protein	Organism	Identities (%)	Coverage (%)	Ha-value
T10021	Lacticaseibacillus rhamnosus 51B	100	100	1
T10020	Lacticaseibacillus rhamnosus strain 24	100	100	1
T6143	Lactobacillus rhamnosus ATCC 8530	100	100	1
T6138	Lactobacillus rhamnosus Lc 705	100	100	1
T6115	Enterococcus faecium	57.647	100	0.576
T6022	Enterococcus faecium	57.647	100	0.576
T728	Streptococcus pneumoniae R6	55.294	100	0.56
T4918	Actinobacillus pleuropneumoniae serovar 3 str. JL03	54.118	98.837	0.535
T6281	Streptococcus suis SC84	55.556	95.294	0.529
T2427	Staphylococcus aureus subsp. aureus NCTC 8325	48.193	96.512	0.465
T613	Staphylococcus aureus subsp. aureus MW2	48.193	96.512	0.465
T6122	Streptomyces coelicolor A3(2)	47.561	97.619	0.464
T1043	Escherichia coli str. K-12 substr. MG1655	48.148	96.429	0.464
T1074	Staphylococcus aureus subsp. aureus N315	46.988	96.512	0.453
T130	Mycobacterium tuberculosis H37Rv	47.436	91.765	0.435
T10072	Edwardsiella tarda EIB202	42.169	96.512	0.407
T10077	Agrobacterium tumefaciens str. C58	39.326	100	0.407
T310	Pseudomonas putida KT2440	43.21	94.186	0.407
T10182	Aggregatibacter actinomycetemcomitans D11S 1	37.805	98.795	0.373

Multiple sequence alignment

Antitoxin

Protein	Organism	Identities (%)	Coverage (%)	Ha-value
AT6138	Lactobacillus rhamnosus Lc 705	100	100	1
AT6143	Lactobacillus rhamnosus ATCC 8530	100	100	1
AT10020	Lacticaseibacillus rhamnosus strain 24	100	100	1
AT10021	Lacticaseibacillus rhamnosus 51B	100	100	1
AT10182	Aggregatibacter actinomycetemcomitans D11S 1	54.118	100	0.548
AT6115	Enterococcus faecium	57.831	93.258	0.539
AT6022	Enterococcus faecium	57.831	93.258	0.539
AT728	Streptococcus pneumoniae R6	47.5	95.238	0.452
AT6281	Streptococcus suis SC84	40.964	96.512	0.395
AT2427	Staphylococcus aureus subsp. aureus NCTC 8325	42.466	87.952	0.373
AT613	Staphylococcus aureus subsp. aureus MW2	42.466	87.952	0.373
AT1074	Staphylococcus aureus subsp. aureus N315	42.466	87.952	0.373
AT4918	Actinobacillus pleuropneumoniae serovar 3 str. JL03	34.94	100	0.349
AT6122	Streptomyces coelicolor A3(2)	37.662	88.506	0.333
AT10077	Agrobacterium tumefaciens str. C58	34.211	90.476	0.31
AT10072	Edwardsiella tarda EIB202	32.895	93.827	0.309
AT310	Pseudomonas putida KT2440	32.927	92.135	0.303

Multiple sequence alignment

Structures

Toxin

• AlphaFold DB: A0A249N526

Antitoxin

• AlphaFold DB: A0A249N594

References

(1) K M Klimina et al. (2013) Identification and characterization of toxin-antitoxin systems in strains of Lactobacillus rhamnosus isolated from humans. Anaerobe 22:82-9. [PubMed:23727113]


 experimental literature