Detailed information of TA system TA024516

Bioinformatically predicted

Overview

TA module

• Type: II
• Classification (family/domain): phd-doc/Doc-RelB
• Location: 4619509..4620095
• Replicon: chromosome
• Accession: NC_013716
• Organism: Citrobacter rodentium ICC168

Toxin (Protein)

• Gene name: doc
• Uniprot ID: D2TLJ0
• Locus tag: ROD_RS21570
• Protein ID: WP_012908306.1
• Coordinates: 4619727..4620095 (+)
• Length: 123 a.a.

Antitoxin (Protein)

• Gene name: phd
• Uniprot ID: D2TLI9
• Locus tag: ROD_RS21565
• Protein ID: WP_012908305.1
• Coordinates: 4619509..4619730 (+)
• Length: 74 a.a.

Genomic Context

Locus tag	Coordinates	Strand	Size (bp)	Protein ID	Product	Description
ROD_RS21540	4614518..4615627	+	1110	WP_012908300.1	high-affinity branched-chain amino acid ABC transporter substrate-binding protein LivK	-
ROD_RS21545	4615689..4616615	+	927	WP_012908301.1	high-affinity branched-chain amino acid ABC transporter permease LivH	-
ROD_RS21550	4616612..4617889	+	1278	WP_012908302.1	branched chain amino acid ABC transporter permease LivM	-
ROD_RS21555	4617886..4618653	+	768	WP_012908303.1	high-affinity branched-chain amino acid ABC transporter ATP-binding protein LivG	-
ROD_RS21560	4618655..4619368	+	714	WP_012908304.1	high-affinity branched-chain amino acid ABC transporter ATP-binding protein LivF	-
ROD_RS21565	4619509..4619730	+	222	WP_012908305.1	type II toxin-antitoxin system Phd/YefM family antitoxin	Antitoxin
ROD_RS21570	4619727..4620095	+	369	WP_012908306.1	type II toxin-antitoxin system death-on-curing family toxin	Toxin
ROD_RS21575	4620334..4621650	+	1317	WP_012908307.1	sn-glycerol-3-phosphate ABC transporter substrate-binding protein UgpB	-
ROD_RS21580	4621751..4622638	+	888	WP_012908308.1	sn-glycerol-3-phosphate ABC transporter permease UgpA	-
ROD_RS21585	4622635..4623480	+	846	WP_012908309.1	sn-glycerol-3-phosphate ABC transporter permease UgpE	-
ROD_RS21590	4623482..4624552	+	1071	WP_012908310.1	sn-glycerol-3-phosphate import ATP-binding protein UgpC	-

Associated MGEs

MGE detail	Similar MGEs	Relative position	MGE Type	Cargo ARG	Virulence gene	Coordinates	Length (bp)
	-	inside	Prophage	-	-	4614518..4625295	10777

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

• Fido domain (26-86)

Antitoxin

• Type II toxin-antitoxin system, antitoxin Phd/YefM (1-53)

Sequences

Toxin

Protein

• Length: 123 a.a.
• Molecular weight: 13598.89 Da
• Isoelectric Point: 7.3180

>T24516 WP_012908306.1 NC_013716:4619727-4620095 [Citrobacter rodentium ICC168]
MSVQFISAEEIVRFHDKLLSVTPGVAGMPDPGRAEALLYRVLNKYEYEGVTDVWLLAAMHLLAISRGHIFNDGNKRTALF
ITLLFLKRNGITLKANPDFVAMTVEAAAGRLSLEEIAELLRR

Nucleotide

• Length: 369 bp

>T24516 NC_013716:4619727-4620095 [Citrobacter rodentium ICC168]
ATGAGTGTGCAATTTATCTCAGCGGAAGAGATAGTCCGGTTTCATGACAAACTGCTGAGCGTCACGCCCGGCGTAGCGGG
AATGCCGGATCCCGGGCGAGCGGAAGCTCTTTTGTATCGTGTCCTGAATAAGTATGAATACGAAGGCGTCACGGATGTCT
GGCTCCTTGCGGCCATGCATCTGTTGGCTATCTCCCGTGGTCATATTTTCAACGACGGCAATAAACGCACAGCCCTGTTC
ATCACCCTGCTTTTTCTCAAACGCAACGGCATTACGCTGAAGGCCAATCCGGATTTTGTGGCGATGACGGTCGAGGCTGC
TGCGGGTCGCTTATCCCTCGAAGAGATTGCTGAGCTTTTACGCCGCTAG

Antitoxin

Protein

• Length: 74 a.a.
• Molecular weight: 8064.07 Da
• Isoelectric Point: 5.6663

>AT24516 WP_012908305.1 NC_013716:4619509-4619730 [Citrobacter rodentium ICC168]
MRTMNYSEARQNLASALDSAATGTPVTITRRGHKPAVIISAEEFERYQAAKLDAEFEAIMAVHGNEIRELADK

Nucleotide

• Length: 222 bp

>AT24516 NC_013716:4619509-4619730 [Citrobacter rodentium ICC168]
ATGCGTACAATGAACTATAGCGAAGCCCGCCAGAATCTTGCTTCCGCACTGGATTCTGCGGCTACCGGAACGCCAGTTAC
CATCACGCGTCGTGGGCATAAGCCCGCCGTCATCATCAGCGCCGAAGAGTTTGAACGCTATCAGGCAGCAAAACTGGATG
CGGAATTTGAGGCGATTATGGCGGTTCATGGAAATGAAATAAGGGAACTGGCTGATAAATGA

Structures

Toxin

• AlphaFold DB: D2TLJ0

Antitoxin

• AlphaFold DB: D2TLI9