Detailed information of TA system TA024790

Bioinformatically predicted

Overview

TA module

• Type: II
• Classification (family/domain): ccdAB/CcdA(antitoxin)
• Location: 82778..83324
• Replicon: chromosome
• Accession: NC_014228
• Organism: Xenorhabdus nematophila ATCC 19061

Toxin (Protein)

• Gene name: ccdB
• Uniprot ID: N1NNP2
• Locus tag: XNC1_RS00380
• Protein ID: WP_010847542.1
• Coordinates: 83019..83324 (+)
• Length: 102 a.a.

Antitoxin (Protein)

• Gene name: ccdA
• Uniprot ID: -
• Locus tag: XNC1_RS00375
• Protein ID: WP_173363083.1
• Coordinates: 82778..83017 (+)
• Length: 80 a.a.

Genomic Context

Locus tag	Coordinates	Strand	Size (bp)	Protein ID	Product	Description
XNC1_RS00350 (XNC1_0075)	79023..79763	-	741	WP_010847535.1	transferrin-binding protein-like solute binding protein	-
XNC1_RS00355 (XNC1_0077)	80396..81160	+	765	WP_013183068.1	hypothetical protein	-
XNC1_RS00360 (XNC1_0078)	81166..81996	-	831	WP_013183069.1	formate dehydrogenase accessory sulfurtransferase FdhD	-
XNC1_RS00365 (XNC1_0079)	82145..82345	+	201	Protein_67	hypothetical protein	-
XNC1_RS00370 (XNC1_0080)	82354..82695	+	342	WP_081480159.1	formate dehydrogenase subunit gamma	-
XNC1_RS00375 (XNC1_0081)	82778..83017	+	240	WP_173363083.1	type II toxin-antitoxin system CcdA family antitoxin	Antitoxin
XNC1_RS00380 (XNC1_0082)	83019..83324	+	306	WP_010847542.1	CcdB family protein	Toxin
XNC1_RS00385 (XNC1_0084)	83427..85505	-	2079	WP_013183074.1	plasmid pRiA4b ORF-3 family protein	-
XNC1_RS00390 (XNC1_0085)	85489..85704	-	216	WP_010847545.1	hypothetical protein	-
XNC1_RS20850 (XNC1_0086)	85742..86050	+	309	WP_010847546.1	formate dehydrogenase accessory protein FdhE	-

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 CcdB (2-100)

Antitoxin

• Post-segregation antitoxin CcdA (9-79)

Sequences

Toxin

Protein

• Length: 102 a.a.
• Molecular weight: 11543.30 Da
• Isoelectric Point: 4.9756

>T24790 WP_010847542.1 NC_014228:83019-83324 [Xenorhabdus nematophila ATCC 19061]
MQYTVYKNTGNPDYSYLLDVQSDIIDVLETRLVIPLFLKSNFHGRIPTRLCPTLNIDGNEYLVMTHAMASIRVSMLGDEM
TNVSSHRQLIKDAMDLLFDGF

Nucleotide

• Length: 306 bp

>T24790 NC_014228:83019-83324 [Xenorhabdus nematophila ATCC 19061]
ATGCAGTACACAGTTTACAAAAATACAGGTAATCCTGATTATTCCTATCTGTTGGATGTTCAGAGCGACATTATTGATGT
ATTAGAAACACGATTGGTCATTCCATTATTCCTAAAATCAAATTTCCACGGGCGAATTCCAACTCGATTATGCCCGACCC
TGAACATTGATGGGAACGAATATCTCGTTATGACTCACGCGATGGCTAGCATCAGAGTCTCTATGTTAGGTGATGAGATG
ACAAATGTTTCATCCCACAGACAGCTAATTAAAGATGCGATGGATTTACTCTTTGACGGGTTTTGA

Antitoxin

Protein

• Length: 80 a.a.
• Molecular weight: 9037.22 Da
• Isoelectric Point: 8.5906

>AT24790 WP_173363083.1 NC_014228:82778-83017 [Xenorhabdus nematophila ATCC 19061]
MTALHSRTKKTVSVTVSPELYEQAKQIGLNFSAILTQALIAELKSAAAEQWKRDNREGFEELNRITREHGLLSDQYRTF

Nucleotide

• Length: 240 bp

>AT24790 NC_014228:82778-83017 [Xenorhabdus nematophila ATCC 19061]
ATGACAGCATTACACTCCAGAACTAAAAAAACCGTCAGCGTGACTGTTTCACCAGAACTGTATGAACAAGCAAAACAAAT
AGGACTAAATTTTTCTGCTATTTTGACTCAGGCATTAATTGCAGAACTTAAATCTGCGGCGGCTGAGCAGTGGAAACGTG
ATAATAGGGAGGGATTCGAAGAACTCAATCGCATCACCCGTGAACATGGTCTACTGTCCGATCAATATAGGACATTTTAA

Structures

Toxin

• AlphaFold DB: N1NNP2