Detailed information of TA system TA006239

Experimentally validated

Overview

TA module

• Type: II
• Classification (family/domain): relBE/RelE(toxin)
• Location: 513085..513570
• Replicon: chromosome
• Accession: NC_017491
• Organism: Lactobacillus rhamnosus ATCC 8530

Toxin (Protein)

• Gene name: relE
• Uniprot ID: C2K0Y1
• Locus tag: LRHK_RS13845
• Protein ID: WP_005691636.1
• Coordinates: 513085..513270 (-)
• Length: 62 a.a.

Antitoxin (Protein)

• Gene name: relB
• Uniprot ID: A0A508YYT1
• Locus tag: LRHK_RS02420
• Protein ID: WP_014571130.1
• Coordinates: 513298..513570 (-)
• Length: 91 a.a.

Genomic Context

Locus tag	Coordinates	Strand	Size (bp)	Protein ID	Product	Description
LRHK_RS02395 (LRHK_518)	508092..508781	+	690	WP_005691628.1	rhomboid family intramembrane serine protease	-
LRHK_RS02400 (LRHK_520)	509273..509881	-	609	WP_005691630.1	hypothetical protein	-
LRHK_RS02410 (LRHK_522)	510328..511203	+	876	WP_024305787.1	XRE family transcriptional regulator	-
LRHK_RS02415 (LRHK_523)	511446..512861	-	1416	WP_005691634.1	DNA polymerase III subunit epsilon	-
LRHK_RS13845 (LRHK_524)	513085..513270	-	186	WP_005691636.1	type II toxin-antitoxin system mRNA interferase toxin, RelE/StbE family	Toxin
LRHK_RS02420 (LRHK_525)	513298..513570	-	273	WP_014571130.1	type II toxin-antitoxin system RelB/DinJ family antitoxin	Antitoxin
LRHK_RS02425 (LRHK_526)	514132..514380	+	249	WP_005691639.1	hypothetical protein	-
LRHK_RS02430 (LRHK_527)	514623..514916	+	294	WP_005684269.1	metalloregulator ArsR/SmtB family transcription factor	-
LRHK_RS02435 (LRHK_528)	514998..516161	+	1164	WP_005691640.1	MFS transporter	-
LRHK_RS02440 (LRHK_529)	516315..516890	+	576	WP_014571131.1	DNA-3-methyladenine glycosylase I	-
LRHK_RS02445 (LRHK_530)	517033..517629	+	597	WP_005691643.1	IS607 family transposase	-

Associated MGEs

MGE detail	Similar MGEs	Relative position	MGE Type	Cargo ARG	Virulence gene	Coordinates	Length (bp)
	Similar MGE(s) Similar MGE(s) is defined as other TA-related MGE(s) with Mash distance < 0.01 to this MGE. Detail Genome accession Organism MGE type Related TA Coordinates Mash distance View NC_013199 Lactobacillus rhamnosus Lc 705 Genomic island TA006139 509097..519119 0 View NC_013199 Lactobacillus rhamnosus Lc 705 Genomic island TA006139 509097..519119 0 View NC_021725 Lactobacillus rhamnosus LOCK908 Genomic island TA029676 517678..527700 0 View NZ_CP019305 Lacticaseibacillus rhamnosus strain SCT-10-10-60 Genomic island TA072233 517689..528892 0.003 View NZ_CP022109 Lacticaseibacillus rhamnosus strain JCM1553 Genomic island TA078456 517689..528892 0.003 View NZ_CP046267 Lacticaseibacillus rhamnosus strain BIO5326 Genomic island TA143788 517678..527700 0 View NZ_CP067365 Lacticaseibacillus rhamnosus strain KF7 Genomic island TA186159 528194..539428 0.003 View NZ_CP073711 Lacticaseibacillus rhamnosus strain X253 Genomic island TA200045 517678..527700 0 View NZ_CP082961 Lacticaseibacillus rhamnosus strain CAU 1365 Genomic island TA215714 2643831..2655034 0.003 View NZ_CP086326 Lacticaseibacillus rhamnosus strain PMC203 Genomic island TA222966 2427363..2438367 0.004 View NZ_CP092033 Lacticaseibacillus rhamnosus strain VHProbi Y39 Genomic island TA235496 517678..527700 0 View NZ_CP099396 Lacticaseibacillus rhamnosus strain P118 Genomic island TA248870 517678..527700 0 View NZ_CP102716 Lacticaseibacillus rhamnosus strain DM065 Genomic island TA254067 2430309..2441313 0.004 View NZ_CP118035 Lacticaseibacillus rhamnosus strain VSI33 Genomic island TA272698 517681..527703 0 View NZ_CP118050 Lacticaseibacillus rhamnosus strain VSI43 Genomic island TA272725 513060..524263 0.003 View NZ_CP118050 Lacticaseibacillus rhamnosus strain VSI43 Genomic island TA272725 513060..525273 0.005 View NZ_CP120736 Lacticaseibacillus rhamnosus strain A5 Genomic island TA275388 325746..336953 0.003 View NZ_LR134322 Lacticaseibacillus rhamnosus strain NCTC13710 Genomic island TA287676 517678..527700 0 View NZ_LR134331 Lacticaseibacillus rhamnosus strain NCTC13764 Genomic island TA287704 518870..528892 0 View NZ_LT220504 Lacticaseibacillus rhamnosus strain BPL5 Genomic island TA293114 1739484..1750488 0.004	inside	Genomic island	-	-	509273..519295	10022

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, RelE/ParE toxin family (8-57)

Antitoxin

• RelB antitoxin/Antitoxin DinJ (6-65)

Sequences

Toxin

Protein

• Length: 62 a.a.
• Molecular weight: 6781.86 Da
• Isoelectric Point: 7.4698

>T6239 WP_005691636.1 NC_017491:c513270-513085 [Lactobacillus rhamnosus ATCC 8530]
MQRQGHVKLASLHDHALKGAHSGERALRVAPDWLLVYKVDAEALILMLLATGTHRDTLNIE

Nucleotide

• Length: 186 bp

>T6239 NC_017491:c513270-513085 [Lactobacillus rhamnosus ATCC 8530]
TTGCAGCGTCAAGGTCATGTAAAATTAGCTTCTCTACATGACCATGCTTTAAAGGGTGCTCACAGCGGCGAACGAGCATT
GCGTGTTGCTCCTGATTGGCTTCTCGTTTATAAAGTCGATGCTGAAGCGTTAATTTTAATGCTTCTTGCAACAGGCACAC
ACCGCGATACATTGAACATTGAGTAA

Antitoxin

Protein

• Length: 91 a.a.
• Molecular weight: 10005.62 Da
• Isoelectric Point: 9.5939

>AT6239 WP_014571130.1 NC_017491:c513570-513298 [Lactobacillus rhamnosus ATCC 8530]
MTKKSRISVRIDTKTKERALHVLNSMGLDISSAINMYLKRIGDTGALPFTPPMSFVDQLQVAEADVKAGRIKSFKTVDAL
MKDLYSDVDD

Nucleotide

• Length: 273 bp

>AT6239 NC_017491:c513570-513298 [Lactobacillus rhamnosus ATCC 8530]
ATGACCAAAAAATCCCGCATCAGCGTTAGGATTGATACCAAAACTAAAGAACGAGCGCTCCATGTTCTTAATAGCATGGG
ATTAGATATTTCCTCGGCTATTAACATGTACCTGAAACGGATTGGTGACACCGGTGCATTGCCATTTACACCTCCAATGT
CATTTGTTGATCAGCTTCAAGTTGCAGAAGCTGATGTTAAAGCGGGGCGAATAAAAAGCTTCAAGACTGTCGATGCTTTG
ATGAAGGATTTATACAGTGATGTTGACGATTAA

Similar Proteins

Only experimentally validated proteins are listed.

Toxin

Protein	Organism	Identities (%)	Coverage (%)	Ha-value
T6139	Lactobacillus rhamnosus Lc 705	100	100	1
T6144	Lactobacillus rhamnosus ATCC 8530	100	100	1
T10110	Lacticaseibacillus rhamnosus strain 1019 DinJ and YafQ genes	100	100	1
T10108	Lacticaseibacillus rhamnosus strain 1473 DinJ and YafQ genes	93.443	100	0.934
T10109	Lacticaseibacillus rhamnosus strain 2360 DinJ and YafQ genes	93.443	100	0.934
T10111	Lacticaseibacillus paracasei strain 4366 DinJ and YafQ genes	46	81.967	0.377
T10112	Lacticaseibacillus paracasei strain 2333 DinJ and YafQ genes	44	81.967	0.361
T6256	Bifidobacterium longum subsp. infantis ATCC 15697 = JCM 1222	50	68.852	0.344
T665	Streptococcus mutans UA159	42	81.967	0.344
T10095	Clostridium difficile R20291	48.837	70.492	0.344
T10070	Tetragenococcus halophilus NBRC 12172	40.816	80.328	0.328
T28	Helicobacter pylori 26695	44.444	73.77	0.328
T6290	Escherichia coli BW25113	42.222	73.77	0.311
T6286	Campylobacter jejuni subsp. jejuni IA3902	42.222	73.77	0.311
T1038	Escherichia coli str. K-12 substr. MG1655	42.222	73.77	0.311
T10190	Pseudomonas sp. strain ANT_J3	39.583	78.689	0.311

Multiple sequence alignment

Antitoxin

Protein	Organism	Identities (%)	Coverage (%)	Ha-value
AT6139	Lactobacillus rhamnosus Lc 705	100	100	1
AT10110	Lacticaseibacillus rhamnosus strain 1019 DinJ and YafQ genes	100	100	1
AT6144	Lactobacillus rhamnosus ATCC 8530	100	100	1
AT10109	Lacticaseibacillus rhamnosus strain 2360 DinJ and YafQ genes	90	100	0.9
AT10108	Lacticaseibacillus rhamnosus strain 1473 DinJ and YafQ genes	75.556	100	0.756
AT10136	Pseudomonas savastanoi	33.333	96.667	0.322
AT10112	Lacticaseibacillus paracasei strain 2333 DinJ and YafQ genes	34.146	92.135	0.315
AT10111	Lacticaseibacillus paracasei strain 4366 DinJ and YafQ genes	32.927	92.135	0.303
AT665	Streptococcus mutans UA159	36	83.333	0.3

Multiple sequence alignment

Structures

Toxin

• AlphaFold DB: A0A7X2J6C9

Antitoxin

• AlphaFold DB: A0A508YYT1

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