Detailed information of TA system TA242652

Bioinformatically predicted

Overview

TA module

• Type: II
• Classification (family/domain): ccdAB/CcdA(antitoxin)
• Location: 31416..31941
• Replicon: plasmid pEC6563-3
• Accession: NZ_CP095859
• Organism: Escherichia coli strain EC6563

Toxin (Protein)

• Gene name: ccdB
• Uniprot ID: V0SSI5
• Locus tag: MYG04_RS25495
• Protein ID: WP_001159868.1
• Coordinates: 31416..31721 (-)
• Length: 102 a.a.

Antitoxin (Protein)

• Gene name: ccdA
• Uniprot ID: S1PPD8
• Locus tag: MYG04_RS25500
• Protein ID: WP_000813634.1
• Coordinates: 31723..31941 (-)
• Length: 73 a.a.

Genomic Context

Locus tag	Coordinates	Strand	Size (bp)	Protein ID	Product	Description
MYG04_RS25480 (MYG04_25480)	27326..28492	-	1167	WP_000772446.1	plasmid-partitioning protein SopA	-
MYG04_RS25485 (MYG04_25485)	29080..29835	-	756	WP_000852146.1	replication initiation protein RepE	-
MYG04_RS25490 (MYG04_25490)	30609..31415	-	807	WP_000016982.1	site-specific integrase	-
MYG04_RS25495 (MYG04_25495)	31416..31721	-	306	WP_001159868.1	type II toxin-antitoxin system toxin CcdB	Toxin
MYG04_RS25500 (MYG04_25500)	31723..31941	-	219	WP_000813634.1	type II toxin-antitoxin system antitoxin CcdA	Antitoxin
MYG04_RS25505 (MYG04_25505)	32532..33020	+	489	WP_011254646.1	hypothetical protein	-
MYG04_RS25510 (MYG04_25510)	33054..34187	-	1134	WP_001542067.1	DUF3800 domain-containing protein	-
MYG04_RS25515 (MYG04_25515)	34354..35127	-	774	WP_000905949.1	hypothetical protein	-
MYG04_RS25520 (MYG04_25520)	35140..35640	-	501	WP_000528931.1	HEPN family nuclease	-
MYG04_RS25525 (MYG04_25525)	35905..36135	+	231	WP_001261278.1	type II toxin-antitoxin system VapB family antitoxin	-
MYG04_RS25530 (MYG04_25530)	36132..36548	+	417	WP_001034046.1	type II toxin-antitoxin system VapC family toxin	-

Associated MGEs

MGE detail	Similar MGEs	Relative position	MGE Type	Cargo ARG	Virulence gene	Coordinates	Length (bp)
	-	inside	Non-Mobilizable plasmid	tet(B) / sitABCD	iucA / iucB / iucC / iucD / iutA	1..63122	63122

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 (2-72)

Sequences

Toxin

Protein

• Length: 102 a.a.
• Molecular weight: 11706.51 Da
• Isoelectric Point: 6.4674

>T242652 WP_001159868.1 NZ_CP095859:c31721-31416 [Escherichia coli]
MQFKVYTYKRESRYRLFVDVQSDIIDTPGRRMVIPLASARLLSDKVSRELYPVVHIGDESWRMMTTDMASVPVSVIGEEV
ADLSHRENDIKNAINLMFWGI

Nucleotide

• Length: 306 bp

>T242652 NZ_OW849083:c75508-75092 [Citrobacter freundii]
GTGAACAAGACCTATATGCTGGACACCAACATCTGCTCATTCATCATGCGCGAGCAGCCGGAAGCCGTCCTGAAGCGCCT
TGAGCAGGCGGTGCTGCGTAACCAGCGCATCGTTGTCTCGGCCATCACCTACTCCGAGATGCGCTTCGGCGCCACCGGCC
CGAAGGCCTCGCCGCGCCACATCGAGCTGGTTGACGCGTTCTGCGCCCGCCTCGATGCCATCCTGCCCTGGGATCGCGCC
GCGGTGGATGCGACCACGGAGATTAAGGTGGCGCTGCGCATGGCCGGCACGCCGATCGGCCCGAACGACACGGCTATTGC
CGGGCACGCCATCGCCGCCGGTGCCGTGCTGGTGACGAATAATACGCGGGAATTTGAGCGGGTACCGGGTCTAGTGCTGG
AAGACTGGGTAAGATAA

Antitoxin

Protein

• Length: 73 a.a.
• Molecular weight: 8372.34 Da
• Isoelectric Point: 4.7405

>AT242652 WP_000813634.1 NZ_CP095859:c31941-31723 [Escherichia coli]
MKQRITVTVDSDSYQLLKAYDVNISGLVSTTMQNEARRLRAERWKAENQEGMAEVARFIEMNGSFADENRDW

Nucleotide

• Length: 219 bp

>AT242652 NZ_OW849083:c75735-75505 [Citrobacter freundii]
ATGAGAACCGTATCTATTTTCAAAAATGGCAACAACCGCGCCATCCGCCTGCCCCGCGATCTGGATTTTGAGGGGGTGAG
CGAGCTGGAGATCGTCCGGGAAGGGGACAGCATCATCCTGCGTCCCGTCCGGCCGACCTGGGGCTCGTTCGCGCAGCTCG
AAAAAGCTGACCCGGACTTTATGGCGGAGCGCGAGGACGTTGTCACCGACGAAGGACGATTTAACCTGTGA

Structures

Toxin

• PDB: 4VUB
• PDB: 2VUB
• PDB: 7EPI
• PDB: 7EPG
• PDB: 3VUB
• PDB: 1X75
• PDB: 1VUB
• PDB: 7EPJ
• PDB: 3HPW
• PDB: 3G7Z

Antitoxin

• PDB: 3TCJ
• PDB: 2H3A
• PDB: 2ADN
• PDB: 2ADL
• PDB: 3HPW
• PDB: 2H3C
• PDB: 3G7Z
• AlphaFold DB: A0A829CQY2