Detailed information of TA system    

insolicoBioinformatically predicted

Overview

TA module


Type II Classification (family/domain) vapBC/VapC-VagC
Location 197362..197987 Replicon plasmid pINV-Y394
Accession NZ_CP030773
Organism Shigella flexneri 1c strain Y394

Toxin (Protein)


Gene name vapC Uniprot ID Q7BEJ1
Locus tag B7485_RS24690 Protein ID WP_000911311.1
Coordinates 197362..197760 (-) Length 133 a.a.

Antitoxin (Protein)


Gene name vapB Uniprot ID Q7BEJ0
Locus tag B7485_RS24695 Protein ID WP_000450531.1
Coordinates 197760..197987 (-) Length 76 a.a.

Genomic Context

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
B7485_RS24665 (B7485_26700) 192962..193912 + 951 WP_004970430.1 virulence factor VirK -
B7485_RS24670 (B7485_26705) 193977..194921 + 945 WP_004996485.1 lauroyl-Kdo(2)-lipid IV(A) myristoyltransferase -
B7485_RS24675 (B7485_26710) 195075..195928 - 854 Protein_234 IS630 family transposase -
B7485_RS24685 (B7485_26720) 197174..197353 + 180 Protein_236 hypothetical protein -
B7485_RS24690 (B7485_26725) 197362..197760 - 399 WP_000911311.1 type II toxin-antitoxin system VapC family toxin Toxin
B7485_RS24695 (B7485_26730) 197760..197987 - 228 WP_000450531.1 toxin-antitoxin system antitoxin VapB Antitoxin

Associated MGEs

MGE
detail		 Similar
MGEs		 Relative
position		 MGE Type Cargo ARG Virulence gene Coordinates Length (bp)
- inside Non-Mobilizable plasmid - icsP/sopA / ospB / ospC4 / ospC4 / ospC2 / ospD2 / ospF / ospD1 / ipgB2 / ospE2 / ospC1 / ospD3/senA / ipaH4.5 / ipaH7.8 / ospC2 / ipaH2.5 / ospC3 / ipaJ / ipaA / ipaD / ipaC / ipaB / ipgC / ipgB1 / ipgA / icsB / ipgD / ipgE / ipgF / mxiG / mxiH / mxiI / mxiJ / mxiK / mxiN / mxiL / mxiM / mxiE / mxiD / mxiC / mxiA / spa15 / spa47 / spa13 / spa32 / spa33 / spa24 / spa9 / spa29 / spa40 / virA / icsA/virG / papC / ospI / ipaH9.8 / ospG / ipaH1.4 / ospE1 / nleE 1..221293 221293


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

(5-125)

Antitoxin

SpoVT-AbrB domain

(7-51)


Sequences

Toxin        


Download         Length: 133 a.a.        Molecular weight: 14817.08 Da        Isoelectric Point: 8.5232

>T107934 WP_000911311.1 NZ_CP030773:c197760-197362 [Shigella flexneri 1c]
MLKFMLDTNICIFTIKNKPASVRERFNLNQGKMCISSVTLMELIYGAEKSQMPERNLAVIEGFVSRIDVLDYDAAAATHT
GQIRAELARQGRPVGPFDQMIAGHARSRGLIIVTNNTREFERVGGLRTEDWS

Download         Length: 399 bp

>T107934 NZ_CP030773:c197760-197362 [Shigella flexneri 1c]
ATGCTGAAGTTTATGCTCGATACCAACATCTGCATTTTTACGATAAAGAACAAACCCGCCAGCGTCAGGGAGCGTTTTAA
CCTGAACCAGGGGAAAATGTGTATCAGTTCGGTCACCCTGATGGAGCTGATATATGGTGCAGAAAAAAGCCAGATGCCTG
AACGTAATCTCGCTGTGATCGAGGGATTTGTTTCCCGCATTGATGTTCTGGATTACGACGCTGCTGCAGCCACACACACC
GGCCAGATAAGAGCAGAACTTGCCCGTCAGGGACGCCCTGTCGGGCCATTTGATCAAATGATCGCAGGTCATGCCCGCAG
TCGGGGGCTGATTATTGTGACTAATAACACCCGGGAATTTGAACGTGTGGGCGGCCTGAGAACTGAAGACTGGAGCTGA

Antitoxin


Download         Length: 76 a.a.        Molecular weight: 8565.62 Da        Isoelectric Point: 4.7513

>AT107934 WP_000450531.1 NZ_CP030773:c197987-197760 [Shigella flexneri 1c]
METTVFLSNRSQAVRLPKAVALPENVKRVEVIAVGRTRIITPAGETWDEWFDGHSVSTDFMDNREQPGMQERESF

Download         Length: 228 bp

>AT107934 NZ_CP030773:c197987-197760 [Shigella flexneri 1c]
ATGGAAACCACCGTATTTCTCAGCAACCGCAGCCAGGCGGTCAGACTGCCAAAAGCGGTTGCATTGCCGGAAAACGTAAA
ACGCGTTGAAGTGATTGCTGTCGGACGAACCAGAATCATTACGCCAGCCGGAGAGACATGGGACGAATGGTTCGACGGAC
ACAGCGTCAGCACCGATTTTATGGATAACAGGGAACAGCCCGGCATGCAGGAAAGGGAGTCATTCTGA

Similar Proteins

Only experimentally validated proteins are listed.

Protein Organism Identities (%) Coverage (%) Ha-value
Protein Organism Identities (%) Coverage (%) Ha-value

Structures

Toxin

Source ID Structure
PDB 3TND
PDB 5ED0
PDB 5ECW
PDB 5ECD
PDB 5ECY

Antitoxin

Source ID Structure
PDB 3TND
AlphaFold DB Q7BEJ0

References