Detailed information of TA system TA123004

Bioinformatically predicted

Overview

TA module

• Type: II
• Classification (family/domain): ccdAB/CcdA(antitoxin)
• Location: 1960284..1960837
• Replicon: chromosome
• Accession: NZ_CP038499
• Organism: Dickeya dianthicola strain LAR.16.03.LID

Toxin (Protein)

• Gene name: ccdB
• Uniprot ID: A0A385XW46
• Locus tag: E4659_RS09070
• Protein ID: WP_024108344.1
• Coordinates: 1960523..1960837 (+)
• Length: 105 a.a.

Antitoxin (Protein)

• Gene name: ccdA
• Uniprot ID: A0A385XYG1
• Locus tag: E4659_RS09065
• Protein ID: WP_024108345.1
• Coordinates: 1960284..1960520 (+)
• Length: 79 a.a.

Genomic Context

Locus tag	Coordinates	Strand	Size (bp)	Protein ID	Product	Description
E4659_RS09030 (E4659_09160)	1955368..1955781	-	414	WP_024108566.1	tautomerase family protein	-
E4659_RS09035 (E4659_09165)	1955846..1956256	-	411	WP_024108567.1	hypothetical protein	-
E4659_RS09040 (E4659_09170)	1956338..1957231	-	894	WP_024108568.1	alpha/beta hydrolase	-
E4659_RS09045 (E4659_09175)	1957240..1958223	-	984	WP_024108569.1	MBL fold metallo-hydrolase	-
E4659_RS09050 (E4659_09180)	1958489..1958974	+	486	WP_024108570.1	helix-turn-helix domain-containing protein	-
E4659_RS09055 (E4659_09185)	1959070..1959204	+	135	Protein_1779	winged helix-turn-helix transcriptional regulator	-
E4659_RS09060 (E4659_09190)	1959226..1959957	+	732	Protein_1780	zincin-like metallopeptidase domain-containing protein	-
E4659_RS09065 (E4659_09195)	1960284..1960520	+	237	WP_024108345.1	type II toxin-antitoxin system CcdA family antitoxin	Antitoxin
E4659_RS09070 (E4659_09200)	1960523..1960837	+	315	WP_024108344.1	CcdB family protein	Toxin
E4659_RS09075 (E4659_09205)	1961480..1961998	+	519	WP_024108343.1	Hcp family type VI secretion system effector	-
E4659_RS09080 (E4659_09210)	1962111..1963967	+	1857	WP_024108342.1	type VI secretion system tip protein VgrG	-
E4659_RS09085	1963993..1964277	+	285	Protein_1785	type VI secretion system PAAR protein	-
E4659_RS09090 (E4659_09220)	1964517..1965392	+	876	WP_024108340.1	DUF6402 family protein	-
E4659_RS09095 (E4659_09225)	1965389..1965820	+	432	WP_071599229.1	DUF6201 family protein	-

Associated MGEs

MGE detail	Similar MGEs	Relative position	MGE Type	Cargo ARG	Virulence gene	Coordinates	Length (bp)
	-	inside	Genomic island	-	hcp	1949146..1975318	26172

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 (2-103)

Antitoxin

• Post-segregation antitoxin CcdA (9-78)

Sequences

Toxin

Protein

• Length: 105 a.a.
• Molecular weight: 11487.43 Da
• Isoelectric Point: 7.9859

>T123004 WP_024108344.1 NZ_CP038499:1960523-1960837 [Dickeya dianthicola]
MQFTVYGNTGKSVVYPLLLDVTSDIIGQLNRRIVIPLLPVEKYPAGRRPDRLVPVVRLTDGKEYAVMTHELASIPVQALG
AVFCDASQYRTQVKAAIDFLIDGI

Nucleotide

• Length: 315 bp

>T123004 NZ_CP038499:1960523-1960837 [Dickeya dianthicola]
ATGCAATTCACCGTATACGGTAATACCGGGAAAAGCGTCGTTTACCCGCTGTTGCTCGATGTCACGAGCGATATTATTGG
ACAGTTGAATCGTCGGATAGTGATCCCGTTGCTCCCTGTTGAAAAGTACCCGGCAGGCCGCCGGCCGGATCGCCTAGTCC
CTGTCGTCAGGCTGACGGACGGCAAAGAGTACGCCGTAATGACGCACGAGCTGGCAAGTATCCCTGTGCAGGCTCTGGGG
GCGGTGTTTTGTGATGCGTCGCAGTACCGTACTCAGGTAAAGGCCGCAATAGATTTCCTCATTGACGGTATTTAG

Antitoxin

Protein

• Length: 79 a.a.
• Molecular weight: 9050.09 Da
• Isoelectric Point: 6.7184

>AT123004 WP_024108345.1 NZ_CP038499:1960284-1960520 [Dickeya dianthicola]
MTAKQRNTQSVTMTVERALLVRAREAGINLSATLTTALDAELRRHEAKKWQEENREAIDALNRFHDEHGCFSDEYRTF

Nucleotide

• Length: 237 bp

>AT123004 NZ_CP038499:1960284-1960520 [Dickeya dianthicola]
ATGACCGCGAAACAGCGCAACACGCAGAGCGTGACCATGACGGTAGAGCGTGCCTTACTGGTCCGGGCGCGTGAGGCGGG
CATTAACCTGAGTGCCACTCTGACAACCGCCCTGGATGCCGAGCTTCGCCGTCATGAAGCGAAAAAATGGCAGGAAGAGA
ACAGGGAAGCCATCGACGCATTAAATCGTTTTCATGATGAGCACGGCTGTTTCAGCGATGAATACCGGACGTTTTAA

Structures

Toxin

• AlphaFold DB: A0A385XW46

Antitoxin

• AlphaFold DB: A0A385XYG1