Detailed information of TA system TA010106

Experimentally validated

Overview

TA module

• Type: II
• Classification (family/domain): hipBA/-
• Location: 4076692..4078242
• Replicon: chromosome
• Accession: NC_014228
• Organism: Xenorhabdus nematophila ATCC 19061

Toxin (Protein)

• Gene name: hipA
• Uniprot ID: D3VDL4
• Locus tag: XNC1_RS17910
• Protein ID: WP_013185548.1
• Coordinates: 4076692..4077990 (-)
• Length: 433 a.a.

Antitoxin (Protein)

• Gene name: hipB
• Uniprot ID: N1NPE2
• Locus tag: XNC1_RS17915
• Protein ID: WP_010847709.1
• Coordinates: 4077991..4078242 (-)
• Length: 84 a.a.

Genomic Context

Locus tag	Coordinates	Strand	Size (bp)	Protein ID	Product	Description
XNC1_RS23040	4072442..4072952	-	511	Protein_3545	N-acetyltransferase	-
XNC1_RS23375 (XNC1_4227)	4072936..4073109	-	174	WP_013185544.1	hypothetical protein	-
XNC1_RS17895 (XNC1_4228)	4073153..4073845	-	693	WP_013185545.1	amino acid racemase	-
XNC1_RS17900 (XNC1_4229)	4073974..4074864	+	891	WP_013185546.1	LysR family transcriptional regulator	-
XNC1_RS17905 (XNC1_4230)	4075019..4076299	-	1281	WP_013185547.1	dicarboxylate/amino acid:cation symporter	-
XNC1_RS17910 (XNC1_4231)	4076692..4077990	-	1299	WP_013185548.1	type II toxin-antitoxin system HipA family toxin	Toxin
XNC1_RS17915 (XNC1_4232)	4077991..4078242	-	252	WP_010847709.1	helix-turn-helix domain-containing protein	Antitoxin
XNC1_RS17920 (XNC1_4233)	4078346..4079083	+	738	Protein_3552	IS630 family transposase	-
XNC1_RS17925 (XNC1_4234)	4079223..4080263	-	1041	WP_013185550.1	IS630 family transposase	-
XNC1_RS17935 (XNC1_4236)	4080959..4081720	+	762	WP_013183573.1	IS5 family transposase	-
XNC1_RS17940 (XNC1_4237)	4081686..4082969	-	1284	WP_013185552.1	serine hydroxymethyltransferase	-

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 NZ_LN681227 Xenorhabdus nematophila AN6/1 Genomic island TA285559 4072040..4087789 0	inside	Genomic island	-	-	4072526..4088275	15749
	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 NZ_CP032329 Xenorhabdus nematophila strain YL001 IS/Tn TA111666 3777140..3778006 0.007 View NZ_CP060401 Xenorhabdus nematophila strain SII IS/Tn TA170338 3777192..3778058 0.007 View NZ_LN681227 Xenorhabdus nematophila AN6/1 IS/Tn TA285559 4078737..4079777 0	flank	IS/Tn	-	-	4079223..4080263	1040

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

• HipA-like, C-terminal (148-397)

Antitoxin

• Cro/C1-type helix-turn-helix domain (13-65)

Sequences

Toxin

Protein

• Length: 433 a.a.
• Molecular weight: 48445.66 Da
• Isoelectric Point: 6.9974

>T10106 WP_013185548.1 NC_014228:c4077990-4076692 [Xenorhabdus nematophila ATCC 19061]
MNKLIVALNGLEVGVLFRDKKGAMSFQYTNEWLKEPGTRAISLSLPLSNQKYVGQEVFNFFDNLLPDSREIIARMQARFQ
ITSKHPFDLLASVGRDCVGAIQLYQEGNQIPPIDEVHAEPLDERAIVELLEGYKTTPLGMNNSDDFRISLAGAQEKTALL
WHQGCWQRPYGSTPTSHIFKLPIGRIEHNNIDLHESCENEWLCLKISRTFGLPVANAELAKFGEKTVLIVERFDRRWSCD
NRWLMRLPQEDMCQAMGIAPALKYEADGGPGIADIMTLLLGSRNSITDRETFFKSQILYWLLAAIDGHGKNFSIFIEPDS
SYSMTPLYDILSAYPIFGAKGVAPKKAKMAMALRGKSRQYHWATIQPRHFPSTARQVGFSESMAEKLMNEMGNMAEKVIN
QVANELPPNFPGHISDAIFTGLAKQAGRLCAG

Nucleotide

• Length: 1299 bp

>T10106 NC_014228:c4077990-4076692 [Xenorhabdus nematophila ATCC 19061]
ATGAACAAATTGATCGTTGCATTGAATGGGCTGGAAGTGGGGGTCTTGTTTCGTGATAAAAAAGGAGCCATGTCTTTCCA
GTACACAAATGAGTGGCTGAAAGAACCCGGTACTCGTGCAATATCACTTTCTTTACCTCTCAGTAACCAGAAATATGTAG
GTCAGGAGGTATTCAATTTCTTCGATAATTTATTACCCGATTCAAGGGAAATCATAGCCCGTATGCAGGCTAGATTTCAG
ATAACCAGTAAGCATCCATTCGATCTCTTAGCCAGTGTTGGGAGGGACTGTGTTGGCGCTATTCAGCTCTATCAGGAAGG
TAATCAAATTCCTCCAATTGACGAGGTTCACGCTGAGCCTTTGGATGAGCGGGCAATAGTCGAGTTGCTTGAAGGCTACA
AGACGACGCCTTTAGGGATGAACAATAGTGACGATTTCCGGATCTCTTTGGCTGGCGCGCAGGAAAAAACAGCCCTTCTA
TGGCATCAAGGCTGTTGGCAGCGACCTTACGGGAGTACGCCTACGAGTCATATATTTAAACTCCCCATAGGCAGAATTGA
GCACAATAATATCGATCTTCACGAGAGTTGTGAAAATGAATGGTTGTGTTTAAAAATCTCCCGAACATTCGGTCTTCCTG
TTGCAAATGCAGAGTTAGCGAAGTTTGGAGAAAAGACAGTATTGATTGTCGAACGTTTTGATCGCCGTTGGTCTTGTGAT
AATCGGTGGTTGATGCGTCTTCCTCAAGAGGATATGTGTCAGGCTATGGGGATTGCTCCTGCTCTTAAATATGAAGCAGA
TGGAGGTCCTGGGATTGCAGATATCATGACGTTGCTACTCGGCTCCAGAAACTCAATAACAGATCGAGAAACGTTTTTTA
AATCCCAAATTCTATATTGGTTATTGGCTGCGATAGATGGACATGGCAAAAATTTCAGCATTTTTATCGAGCCAGATTCG
TCTTACTCGATGACTCCTCTTTATGATATTTTGTCAGCTTATCCTATCTTTGGTGCTAAGGGAGTTGCTCCAAAGAAAGC
AAAAATGGCGATGGCTTTACGTGGTAAGAGTCGCCAGTATCATTGGGCTACCATTCAACCCAGACATTTTCCAAGTACTG
CTCGTCAGGTTGGTTTTTCTGAATCAATGGCTGAAAAGCTGATGAACGAGATGGGAAATATGGCCGAAAAGGTAATAAAC
CAAGTAGCTAATGAGCTGCCACCTAATTTTCCCGGTCATATCAGCGATGCAATTTTTACTGGTTTGGCTAAACAAGCGGG
CAGGCTTTGTGCAGGGTAA

Antitoxin

Protein

• Length: 84 a.a.
• Molecular weight: 9479.82 Da
• Isoelectric Point: 10.9422

>AT10106 WP_010847709.1 NC_014228:c4078242-4077991 [Xenorhabdus nematophila ATCC 19061]
MKITSPQTLAVAIREQRKKKRLTQKDTADRVGIKQSTVSGFENSPEKSKLETLFKLLSSLGLELQVTERNGSTKSDSRWT
REW

Nucleotide

• Length: 252 bp

>AT10106 NC_014228:c4078242-4077991 [Xenorhabdus nematophila ATCC 19061]
ATGAAGATCACATCACCACAAACACTGGCTGTAGCAATCAGGGAACAGCGCAAAAAAAAGCGCCTGACCCAAAAAGACAC
TGCTGATCGGGTTGGAATAAAGCAGAGTACCGTTTCTGGATTTGAAAACAGTCCGGAAAAAAGCAAGCTGGAAACCTTGT
TTAAATTGCTTTCTTCGCTAGGTTTGGAACTGCAAGTTACAGAGCGCAATGGTTCAACAAAGTCAGATAGTCGCTGGACA
AGGGAGTGGTAA

Similar Proteins

Only experimentally validated proteins are listed.

Toxin

Protein	Organism	Identities (%)	Coverage (%)	Ha-value
T10098	Escherichia coli Nissle 1917	44.828	100	0.451
T1040	Escherichia coli str. K-12 substr. MG1655	44.495	100	0.449
T6108	Burkholderia pseudomallei K96243	44.368	100	0.447
T10104	Caulobacter crescentus NA1000	31.477	97.636	0.307

Multiple sequence alignment

Antitoxin

Protein	Organism	Identities (%)	Coverage (%)	Ha-value
AT10195	Escherichia coli strain BL21 (TaKaRa)	40.964	100	0.41
AT1040	Escherichia coli str. K-12 substr. MG1655	40.964	100	0.41
AT10098	Escherichia coli Nissle 1917	39.759	100	0.398
AT10050	Mycobacterium tuberculosis H37Rv	42.857	75.904	0.325
AT658	Shewanella oneidensis MR-1	34.286	89.744	0.308
AT10036	Legionella pneumophila subsp. pneumophila str. Philadelphia 1	30.097	100	0.304

Multiple sequence alignment

Structures

Toxin

• AlphaFold DB: D3VDL4

Antitoxin

• AlphaFold DB: N1NPE2

References

(1) Mohit Yadav et al. (2020) The hipBA^Xn operon from Xenorhabdus nematophila functions as a bonafide toxin-antitoxin module. Applied Microbiology And Biotechnology 104(7):3081-3095. [PubMed:32043192]


 experimental literature