Detailed information of TA system TA000652

Experimentally validated

Overview

TA module

• Type: II
• Classification (family/domain): vapBC/AbrB-PIN
• Location: 1007753..1008381
• Replicon: chromosome
• Accession: NC_004342
• Organism: Leptospira interrogans serovar Lai str. 56601

Toxin (Protein)

• Gene name: vapC
• Uniprot ID: Q8F7E4
• Locus tag: LA_RS04175
• Protein ID: WP_000281042.1
• Coordinates: 1007923..1008321 (-)
• Length: 133 a.a.

Antitoxin (Protein)

• Gene name: vapB
• Uniprot ID: Q8F7E3
• Locus tag: LA_RS04180
• Protein ID: WP_001192482.1
• Coordinates: 1008321..1008551 (-)
• Length: 77 a.a.

Genomic Context

Location: 1003215..1003982 (768 bp)
Type: Others
Protein ID: WP_000636952.1

Location: 1004523..1005383 (861 bp)
Type: Others
Protein ID: WP_000682233.1

Location: 1011496..1012569 (1074 bp)
Type: Others
Protein ID: WP_000445690.1

Location: 1005600..1006058 (459 bp)
Type: Others
Protein ID: WP_001239004.1

Location: 1006059..1007135 (1077 bp)
Type: Others
Protein ID: WP_001170569.1

Location: 1007277..1007825 (549 bp)
Type: Others
Protein ID: WP_000479564.1

Location: 1007923..1008321 (399 bp)
Type: Toxin
Protein ID: WP_000281042.1

Location: 1008321..1008551 (231 bp)
Type: Antitoxin
Protein ID: WP_001192482.1

Location: 1008799..1009476 (678 bp)
Type: Others
Protein ID: WP_000071998.1

Location: 1009708..1010397 (690 bp)
Type: Others
Protein ID: WP_000590463.1

Location: 1010623..1011246 (624 bp)
Type: Others
Protein ID: Protein_828

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Locus tag	Coordinates	Strand	Size (bp)	Protein ID	Product	Description
LA_RS04150 (LA0996)	1003215..1003982	+	768	WP_000636952.1	DUF1554 domain-containing protein	-
LA_RS04155 (LA0997)	1004523..1005383	+	861	WP_000682233.1	hypothetical protein	-
LA_RS04160 (LA0997a)	1005600..1006058	-	459	WP_001239004.1	GNAT family N-acetyltransferase	-
LA_RS04165 (LA0999)	1006059..1007135	-	1077	WP_001170569.1	hypothetical protein	-
LA_RS04170 (LA1000)	1007277..1007825	-	549	WP_000479564.1	hypothetical protein	-
LA_RS04175 (LA1001)	1007923..1008321	-	399	WP_000281042.1	type II toxin-antitoxin system VapC family toxin	Toxin
LA_RS04180 (LA1002)	1008321..1008551	-	231	WP_001192482.1	AbrB/MazE/SpoVT family DNA-binding domain-containing protein	Antitoxin
LA_RS04185 (LA1003)	1008799..1009476	-	678	WP_000071998.1	hypothetical protein	-
LA_RS04190 (LA1004)	1009708..1010397	-	690	WP_000590463.1	SH3 domain-containing protein	-
LA_RS04195 (LA1005)	1010623..1011246	-	624	Protein_828	M20/M25/M40 family metallo-hydrolase	-
LA_RS04200 (LA1006)	1011496..1012569	+	1074	WP_000445690.1	IS110-like element ISLin1 family transposase	-

Associated MGEs

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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_017551 Leptospira interrogans serovar Lai str. IPAV IS/Tn TA026989 1010888..1011961 0	flank	IS/Tn	-	-	1011496..1012569	1073

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

• PIN domain (2-123)

Antitoxin

• SpoVT-AbrB domain (7-51)

Sequences

Toxin

Protein

• Length: 133 a.a.
• Molecular weight: 15139.76 Da
• Isoelectric Point: 9.6893

>T652 WP_000281042.1 NC_004342:c1008321-1007923 [Leptospira interrogans serovar Lai str. 56601]
MYLLDTNICIFLIKKKNATLLENLKKKLNKDLFVSSLTVAELEFGIQKSEFKEKNKVALIEFLTIFNILSFSDKDAESYG
IIRADLERKGNVIGSIDMLLAAQAIANNYIFVTNNTKEFKRIKALKIENWTQ

Nucleotide

• Length: 399 bp

>T652 NC_004342:c1008321-1007923 [Leptospira interrogans serovar Lai str. 56601]
ATGTATCTTTTGGATACCAATATATGCATTTTTCTAATTAAAAAGAAAAATGCGACTCTGTTAGAAAATCTTAAGAAAAA
ATTAAATAAAGATCTATTTGTTTCGTCTTTAACTGTTGCGGAACTTGAGTTTGGAATTCAGAAAAGTGAATTTAAAGAAA
AGAATAAAGTTGCACTAATCGAATTTTTAACGATTTTCAATATACTTTCCTTTTCTGATAAAGATGCAGAGTCTTACGGT
ATCATCAGAGCGGATTTGGAGAGGAAAGGTAATGTAATCGGTTCAATAGACATGTTACTTGCCGCTCAAGCAATTGCTAA
TAATTATATCTTTGTTACTAATAATACAAAAGAATTTAAAAGAATTAAGGCTTTAAAAATAGAAAATTGGACACAGTAG

Antitoxin

Protein

• Length: 77 a.a.
• Molecular weight: 8771.05 Da
• Isoelectric Point: 8.6588

>AT652 WP_001192482.1 NC_004342:c1008551-1008321 [Leptospira interrogans serovar Lai str. 56601]
MQTAKLFINGRSQAVRLPKEFQFTGDDVLIQKVGEAVILVPKNKAWNVFLEGLNGFSDDFFKEEREQPKSDKREKL

Nucleotide

• Length: 231 bp

>AT652 NC_004342:c1008551-1008321 [Leptospira interrogans serovar Lai str. 56601]
ATGCAAACAGCCAAATTATTTATAAATGGAAGAAGTCAAGCGGTTCGACTACCAAAAGAATTTCAATTTACCGGAGATGA
TGTTCTTATCCAAAAAGTTGGAGAGGCGGTAATATTGGTTCCGAAAAACAAGGCCTGGAACGTATTTTTAGAAGGATTGA
ACGGGTTTTCAGATGATTTCTTTAAGGAGGAGAGAGAACAGCCGAAATCTGATAAAAGAGAAAAGCTTTAA

Similar Proteins

Only experimentally validated proteins are listed.

Toxin

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Protein	Organism	Identities (%)	Coverage (%)	Ha-value
T962	Synechocystis sp. PCC 6803	46.053	91.566	0.422
T3856	Dichelobacter nodosus VCS1703A	42.188	96.97	0.409
T3858	Dichelobacter nodosus VCS1703A	42.188	96.97	0.409
T1070	Haemophilus influenzae Rd KW20	41.538	98.485	0.409
T4922	Actinobacillus pleuropneumoniae serovar 3 str. JL03	40.769	98.485	0.402
T10054	Bosea sp. PAMC 26642 strain PAMC26642	41.085	97.727	0.402
T439	Salmonella enterica subsp. enterica serovar Typhimurium str. LT2	36.364	100	0.364
T1066	Haemophilus influenzae Rd KW20	35.036	100	0.364
T10129	Haemophilus influenzae strain 69P2H1 N69P2H1_45_2	35.036	100	0.364
T877	Sinorhizobium meliloti 1021	35.606	100	0.356

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Multiple sequence alignment

Antitoxin

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Protein	Organism	Identities (%)	Coverage (%)	Ha-value
AT3856	Dichelobacter nodosus VCS1703A	52.703	97.368	0.513
AT3858	Dichelobacter nodosus VCS1703A	52.703	97.368	0.513
AT962	Synechocystis sp. PCC 6803	45.333	100	0.453
AT10054	Bosea sp. PAMC 26642 strain PAMC26642	42.308	100	0.434
AT439	Salmonella enterica subsp. enterica serovar Typhimurium str. LT2	42.105	100	0.427
AT4922	Actinobacillus pleuropneumoniae serovar 3 str. JL03	42.667	98.684	0.421
AT1070	Haemophilus influenzae Rd KW20	38.462	100	0.395
AT1066	Haemophilus influenzae Rd KW20	36.842	100	0.368
AT10129	Haemophilus influenzae strain 69P2H1 N69P2H1_45_2	36.842	100	0.368
AT6111	uncultured bacterium	36.986	96.053	0.355

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Multiple sequence alignment

Structures

Toxin

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• AlphaFold DB: A0A0F6HAN6

Antitoxin

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• AlphaFold DB: A0A0F6HAF7

References

(1) Yi Xuan Zhang et al. (2004) Characterization of a novel toxin-antitoxin module, VapBC, encoded by Leptospira interrogans chromosome. Cell Research 14(3):208-16. [PubMed:15225414]

(2) Alexandre P Y Lopes et al. (2014) VapC from the leptospiral VapBC toxin-antitoxin module displays ribonuclease activity on the initiator tRNA. PloS One 9(7):e101678. [PubMed:25047537]


 experimental literature