Detailed information of TA system TA003858

Experimentally validated

Overview

TA module

• Type: II
• Classification (family/domain): vapBC/AbrB-PIN
• Location: 1076865..1077499
• Replicon: chromosome
• Accession: NC_009446
• Organism: Dichelobacter nodosus VCS1703A

Toxin (Protein)

• Gene name: vapC
• Uniprot ID: -
• Locus tag: DNO_RS05125
• Protein ID: WP_119185609.1
• Coordinates: 1077098..1077499 (+)
• Length: 134 a.a.

Antitoxin (Protein)

• Gene name: vapB
• Uniprot ID: Q46558
• Locus tag: DNO_RS05120
• Protein ID: WP_012030622.1
• Coordinates: 1076865..1077095 (+)
• Length: 77 a.a.

Genomic Context

Locus tag	Coordinates	Strand	Size (bp)	Protein ID	Product	Description
DNO_RS05100 (DNO_1037)	1072982..1074121	+	1140	WP_012031349.1	acyltransferase	-
DNO_RS05105 (DNO_1038)	1074787..1075281	-	495	WP_012031350.1	integrase arm-type DNA-binding domain-containing protein	-
DNO_RS05110 (DNO_1039)	1075930..1076208	+	279	WP_041729404.1	type II toxin-antitoxin system RelE/ParE family toxin	-
DNO_RS05115 (DNO_1040)	1076221..1076529	+	309	WP_012030621.1	HigA family addiction module antidote protein	-
DNO_RS05120 (DNO_1041)	1076865..1077095	+	231	WP_012030622.1	AbrB/MazE/SpoVT family DNA-binding domain-containing protein	Antitoxin
DNO_RS05125 (DNO_1042)	1077098..1077499	+	402	WP_119185609.1	type II toxin-antitoxin system VapC family toxin	Toxin
DNO_RS05130	1078259..1078540	-	282	WP_012030611.1	virulence protein	-
DNO_RS05135 (DNO_1043)	1079043..1080356	-	1314	WP_012031351.1	virulence-associated E family protein	-
DNO_RS05140 (DNO_1044)	1080452..1080673	-	222	WP_012031352.1	hypothetical protein	-
DNO_RS05145 (DNO_1045)	1081068..1082273	-	1206	WP_012031353.1	tyrosine-type recombinase/integrase	-

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

• PIN domain (4-124)

Antitoxin

• SpoVT-AbrB domain (7-51)

Sequences

Toxin

Protein

• Length: 134 a.a.
• Molecular weight: 14910.39 Da
• Isoelectric Point: 7.8485

>T3858 WP_119185609.1 NC_009446:1077098-1077499 [Dichelobacter nodosus VCS1703A]
IKLMLDTNICIYIINRKPPYIAEKFSRYEIGDIGISNITACELAFGVEKSGSAKNKTALTKFLAPLSILPFDKQAIWHYA
RIRQSLQNRGTPIGALDMLIASHALALDITLVTNNTKEFERVDGLMLDNWVID

Nucleotide

• Length: 402 bp

>T3858 NC_009446:1077098-1077499 [Dichelobacter nodosus VCS1703A]
ATCAAATTAATGCTTGATACCAATATCTGCATTTATATCATCAATCGAAAACCGCCATATATTGCCGAAAAATTTTCGCG
ATATGAAATAGGCGATATTGGTATATCTAACATTACCGCTTGTGAGCTTGCGTTTGGCGTAGAAAAATCAGGTTCAGCAA
AAAACAAAACCGCATTAACAAAATTTTTGGCACCACTATCAATATTGCCTTTTGATAAACAAGCTATTTGGCATTACGCA
CGAATCCGACAATCACTGCAAAACCGCGGTACCCCTATCGGGGCTTTAGATATGCTTATCGCTAGCCATGCATTGGCGCT
TGATATCACGTTGGTAACAAATAACACCAAAGAATTTGAACGCGTTGATGGGTTGATGTTAGATAATTGGGTGATAGATT
AA

Antitoxin

Protein

• Length: 77 a.a.
• Molecular weight: 8899.23 Da
• Isoelectric Point: 5.0959

>AT3858 WP_012030622.1 NC_009446:1076865-1077095 [Dichelobacter nodosus VCS1703A]
MKVAKVFTTGRSQAVRIPKAFQFDTKEVIIQRFGNGILLIPKNSDWQGFLEALNEFEPDFKIEREPQIEQVREDFL

Nucleotide

• Length: 231 bp

>AT3858 NC_009446:1076865-1077095 [Dichelobacter nodosus VCS1703A]
ATGAAAGTAGCCAAAGTCTTTACTACGGGGCGCTCGCAAGCGGTTCGCATTCCTAAGGCGTTCCAATTTGATACAAAAGA
GGTAATTATTCAGCGTTTCGGCAACGGAATTTTATTAATCCCTAAAAATTCGGATTGGCAAGGTTTTCTGGAAGCACTCA
ATGAGTTTGAGCCTGATTTTAAAATTGAGCGTGAGCCGCAAATAGAACAAGTGCGGGAAGACTTTTTATGA

Similar Proteins

Only experimentally validated proteins are listed.

Toxin

Protein	Organism	Identities (%)	Coverage (%)	Ha-value
T3856	Dichelobacter nodosus VCS1703A	100	100	1
T962	Synechocystis sp. PCC 6803	48.193	100	0.482
T10054	Bosea sp. PAMC 26642 strain PAMC26642	44.961	97.727	0.439
T4922	Actinobacillus pleuropneumoniae serovar 3 str. JL03	44.186	97.727	0.432
T652	Leptospira interrogans serovar Lai str. 56601	42.188	96.97	0.409
T1070	Haemophilus influenzae Rd KW20	40.909	100	0.409
T439	Salmonella enterica subsp. enterica serovar Typhimurium str. LT2	41.221	99.242	0.409
T877	Sinorhizobium meliloti 1021	42.188	96.241	0.406
T10197	Klebsiella pneumoniae	40.152	99.248	0.399
T6112	uncultured bacterium	38.931	98.496	0.383
T6111	uncultured bacterium	38.636	99.248	0.383
T10129	Haemophilus influenzae strain 69P2H1 N69P2H1_45_2	36.434	96.992	0.353
T1066	Haemophilus influenzae Rd KW20	35.659	96.992	0.346
T4914	Actinobacillus pleuropneumoniae serovar 3 str. JL03	33.858	98.45	0.333

Multiple sequence alignment

Antitoxin

Protein	Organism	Identities (%)	Coverage (%)	Ha-value
AT3856	Dichelobacter nodosus VCS1703A	100	100	1
AT652	Leptospira interrogans serovar Lai str. 56601	52.703	97.368	0.513
AT10054	Bosea sp. PAMC 26642 strain PAMC26642	39.474	100	0.395
AT962	Synechocystis sp. PCC 6803	38.667	100	0.387
AT4922	Actinobacillus pleuropneumoniae serovar 3 str. JL03	37.838	97.368	0.368
AT1070	Haemophilus influenzae Rd KW20	36.111	94.737	0.342
AT10129	Haemophilus influenzae strain 69P2H1 N69P2H1_45_2	43.86	75	0.329
AT1066	Haemophilus influenzae Rd KW20	43.86	75	0.329
AT6111	uncultured bacterium	37.879	86.842	0.329
AT439	Salmonella enterica subsp. enterica serovar Typhimurium str. LT2	33.333	96	0.32
AT6112	uncultured bacterium	36.364	86.842	0.316
AT10197	Klebsiella pneumoniae	36.364	86.842	0.316
AT4914	Actinobacillus pleuropneumoniae serovar 3 str. JL03	38.71	81.579	0.316

Multiple sequence alignment

Structures

Antitoxin

• AlphaFold DB: A5EW96

References

(1) B F Cheetham et al. (1995) Identification of a gene encoding a bacteriophage-related integrase in a vap region of the Dichelobacter nodosus genome. Gene 162(1):53-8. [PubMed:7557417]


 experimental literature