Detailed information of TA system TA108546

Bioinformatically predicted

Overview

TA module

• Type: II
• Classification (family/domain): vapBC/VapC-VagC
• Location: 3005168..3005811
• Replicon: chromosome
• Accession: NZ_CP031146
• Organism: Pseudomonas plecoglossicida strain XSDHY-P

Toxin (Protein)

• Gene name: vapC
• Uniprot ID: S2JTH3
• Locus tag: DVB73_RS13865
• Protein ID: WP_016395192.1
• Coordinates: 3005398..3005811 (+)
• Length: 138 a.a.

Antitoxin (Protein)

• Gene name: vapB
• Uniprot ID: S2KM81
• Locus tag: DVB73_RS13860
• Protein ID: WP_016395191.1
• Coordinates: 3005168..3005398 (+)
• Length: 77 a.a.

Genomic Context

Locus tag	Coordinates	Strand	Size (bp)	Protein ID	Product	Description
DVB73_RS13840	3000630..3001946	-	1317	WP_016395187.1	precorrin-3B synthase	-
DVB73_RS13845	3002064..3003275	+	1212	WP_016395188.1	bifunctional cobalt-precorrin-7 (C(5))-methyltransferase/cobalt-precorrin-6B (C(15))-methyltransferase	-
DVB73_RS13850	3003268..3004362	+	1095	WP_016395189.1	cobalt-precorrin-5B (C(1))-methyltransferase	-
DVB73_RS13855	3004359..3005078	+	720	WP_016395190.1	cobalt-precorrin-6A reductase	-
DVB73_RS13860	3005168..3005398	+	231	WP_016395191.1	antitoxin	Antitoxin
DVB73_RS13865	3005398..3005811	+	414	WP_016395192.1	tRNA(fMet)-specific endonuclease VapC	Toxin
DVB73_RS13870	3005932..3006369	+	438	WP_016395193.1	NfeD family protein	-
DVB73_RS13875	3006397..3007251	+	855	WP_016395194.1	SPFH/Band 7/PHB domain protein	-
DVB73_RS13880	3007458..3007847	+	390	WP_016395195.1	DUF2946 domain-containing protein	-
DVB73_RS13885	3007896..3008381	+	486	WP_016395196.1	copper chaperone PCu(A)C	-
DVB73_RS13890	3008408..3008839	+	432	WP_016395197.1	DUF2946 domain-containing protein	-

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

• PIN domain (4-124)

Antitoxin

• SpoVT-AbrB domain (7-53)

Sequences

Toxin

Protein

• Length: 138 a.a.
• Molecular weight: 15369.69 Da
• Isoelectric Point: 6.9793

>T108546 WP_016395192.1 NZ_CP031146:3005398-3005811 [Pseudomonas plecoglossicida]
MLRYMLDTNICILTIKNKPQVVREAFNRHHGQMAISTVTLMELIYGAEKSAHPERNLSIVESFAARLEVLDYDSRAAEHS
GQLRAELAMAGTPIGPFDQLIAGHARARGLVLVTNNLREFQRVPGLRMEDWLDTPTA

Nucleotide

• Length: 414 bp

>T108546 NZ_CP031146:3005398-3005811 [Pseudomonas plecoglossicida]
ATGCTCAGGTACATGCTCGACACGAATATCTGCATCCTCACCATCAAGAACAAGCCGCAAGTGGTTCGTGAGGCATTCAA
CCGCCATCATGGTCAGATGGCAATCAGTACCGTAACACTGATGGAGCTCATCTACGGCGCGGAAAAGTCAGCCCACCCCG
AGCGTAACCTTTCGATAGTTGAAAGCTTCGCCGCTCGCCTTGAGGTCCTCGACTATGACAGCCGGGCTGCGGAGCACAGT
GGCCAGTTGAGAGCTGAATTGGCAATGGCTGGCACGCCGATCGGCCCCTTCGACCAGTTGATTGCCGGCCATGCGCGCGC
ACGAGGGCTCGTTCTGGTAACAAACAACCTGCGTGAATTCCAGCGAGTCCCTGGTCTTCGCATGGAAGACTGGCTGGATA
CACCGACAGCCTAG

Antitoxin

Protein

• Length: 77 a.a.
• Molecular weight: 8409.28 Da
• Isoelectric Point: 4.2545

>AT108546 WP_016395191.1 NZ_CP031146:3005168-3005398 [Pseudomonas plecoglossicida]
MDQGAVFKSNRSQAIRLPKSVALPEEVTRVDIVAVGRARIITPAGESWDTWFDGDDASPDFMASRDQPADQEREGF

Nucleotide

• Length: 231 bp

>AT108546 NZ_CP031146:3005168-3005398 [Pseudomonas plecoglossicida]
ATGGATCAAGGTGCTGTCTTCAAAAGCAACCGTAGCCAGGCCATCCGCTTGCCGAAATCCGTCGCCCTTCCCGAAGAAGT
GACCCGCGTAGACATCGTTGCTGTGGGACGTGCACGTATCATCACGCCTGCCGGAGAATCGTGGGACACGTGGTTTGACG
GCGATGACGCGAGTCCCGACTTCATGGCCAGCCGCGATCAACCTGCCGACCAGGAACGCGAAGGGTTCTAA

Structures

Toxin

• AlphaFold DB: S2JTH3

Antitoxin

• AlphaFold DB: S2KM81