Detailed information of TA system TA161393

Bioinformatically predicted

Overview

TA module

• Type: II
• Classification (family/domain): ccdAB/CcdA(antitoxin)
• Location: 94081..94606
• Replicon: plasmid unnamed1
• Accession: NZ_CP055076
• Organism: Shigella flexneri strain SWHIN_116

Toxin (Protein)

• Gene name: ccdB
• Uniprot ID: V0SSI5
• Locus tag: HUZ90_RS23350
• Protein ID: WP_001159868.1
• Coordinates: 94081..94386 (-)
• Length: 102 a.a.

Antitoxin (Protein)

• Gene name: ccdA
• Uniprot ID: S1PPD8
• Locus tag: HUZ90_RS23355
• Protein ID: WP_000813634.1
• Coordinates: 94388..94606 (-)
• Length: 73 a.a.

Genomic Context

Locus tag	Coordinates	Strand	Size (bp)	Protein ID	Product	Description
HUZ90_RS23335 (HUZ90_23105)	89991..91157	-	1167	WP_000772446.1	plasmid-partitioning protein SopA	-
HUZ90_RS23340 (HUZ90_23110)	91745..92500	-	756	WP_000852146.1	replication initiation protein RepE	-
HUZ90_RS23345 (HUZ90_23115)	93274..94080	-	807	WP_000016982.1	site-specific integrase	-
HUZ90_RS23350 (HUZ90_23120)	94081..94386	-	306	WP_001159868.1	type II toxin-antitoxin system toxin CcdB	Toxin
HUZ90_RS23355 (HUZ90_23125)	94388..94606	-	219	WP_000813634.1	type II toxin-antitoxin system antitoxin CcdA	Antitoxin
HUZ90_RS23360 (HUZ90_23130)	95173..95685	+	513	WP_000151784.1	hypothetical protein	-
HUZ90_RS23365 (HUZ90_23135)	95719..96852	-	1134	WP_001542067.1	DUF3800 domain-containing protein	-
HUZ90_RS23370 (HUZ90_23140)	97019..97792	-	774	WP_000905949.1	hypothetical protein	-
HUZ90_RS23375 (HUZ90_23145)	97805..98305	-	501	WP_000528931.1	HEPN family nuclease	-
HUZ90_RS23380 (HUZ90_23150)	98570..98800	+	231	WP_001261278.1	type II toxin-antitoxin system VapB family antitoxin	-
HUZ90_RS23385 (HUZ90_23155)	98797..99213	+	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) / catA1 / mph(A) / sul1 / qacE / aadA5 / blaTEM-1B / sul2 / aph(3'')-Ib / aph(6)-Id / aph(3')-Ia / aac(3)-IId / sitABCD	iutA / iucD / iucC / iucB / iucA	1..125787	125787

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

>T161393 WP_001159868.1 NZ_CP055076:c94386-94081 [Shigella flexneri]
MQFKVYTYKRESRYRLFVDVQSDIIDTPGRRMVIPLASARLLSDKVSRELYPVVHIGDESWRMMTTDMASVPVSVIGEEV
ADLSHRENDIKNAINLMFWGI

Nucleotide

• Length: 306 bp

>T161393 NZ_CP071150:4587296-4587679 [Klebsiella pneumoniae]
ATGACCTCCGGATCTGCGCTTTTTGATACCAATATTCTTATTGATTTATTTAGCGGGCGTCGCGAAGCCAAACAGGCGCT
GGAGGCCTGGCCACCGCAGAATGCGATCAGTCTGATTACCTGGATGGAGGTGATGGTTGGCGCTAAAAAATATCACCAGG
AGCAGCGCACGCGAATGGCGCTGAGCACCTTTAATATCATTAACATCTCACAGGATATTGCAGAGCGAAGCGTTGCGCTG
CGGCAGGAGTATAAGCTTAAGCTGCCGGATGCCATCATTCTGGCGACGGCGCAACTCCATCGTCTGGAACTAATTACGCG
GAATACGAAGGATTTTGCCGGTATTCCTGGCGTAGTCACGCCGTACGAAATCCACCCTGAATAA

Antitoxin

Protein

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

>AT161393 WP_000813634.1 NZ_CP055076:c94606-94388 [Shigella flexneri]
MKQRITVTVDSDSYQLLKAYDVNISGLVSTTMQNEARRLRAERWKAENQEGMAEVARFIEMNGSFADENRDW

Nucleotide

• Length: 219 bp

>AT161393 NZ_CP071150:4587054-4587296 [Klebsiella pneumoniae]
ATGATGGCTGAAAGGGATATGGGCAGAATTCTTCTCGATTTATCAGACGATGTCATTCAACGTCTCGATGACCTCAAAGT
GCAGCGTAACATTCCGCGAGCGGAACTGTTACGTGAAGCGGTTGAACAATATCTGGAGAAACAAGATCGAGCTAAAGATA
CCATCTCCAGTGCGCTGGGTCTGTGGCAAGACTGCGAAGAAGACGGCATGGAATATCAACGTCAGCTACGCAAGGAGTGG
TAA

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