Detailed information of TA system    

insolicoBioinformatically predicted

Overview

TA module


Type I Classification (family/domain) ldrD-rdlD/Ldr(toxin)
Location 4079055..4079276 Replicon chromosome
Accession NZ_CP041513
Organism Shigella boydii strain KCCM 41690

Toxin (Protein)


Gene name ldrD Uniprot ID S1PGT3
Locus tag FNA65_RS22205 Protein ID WP_000170954.1
Coordinates 4079055..4079162 (-) Length 36 a.a.

Antitoxin (RNA)


Gene name rdlD
Locus tag -
Coordinates 4079210..4079276 (+)

Genomic Context

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
FNA65_RS22180 4074899..4075981 + 1083 WP_000804740.1 peptide chain release factor 1 -
FNA65_RS22185 4075981..4076814 + 834 WP_000456467.1 peptide chain release factor N(5)-glutamine methyltransferase -
FNA65_RS22190 4076811..4077203 + 393 WP_000200378.1 invasion regulator SirB2 -
FNA65_RS22195 4077207..4078016 + 810 WP_001257044.1 invasion regulator SirB1 -
FNA65_RS22200 4078052..4078906 + 855 WP_000811065.1 3-deoxy-8-phosphooctulonate synthase -
FNA65_RS22205 4079055..4079162 - 108 WP_000170954.1 type I toxin-antitoxin system toxin Ldr family protein Toxin
- 4079210..4079276 + 67 NuclAT_39 - Antitoxin
- 4079210..4079276 + 67 NuclAT_39 - Antitoxin
- 4079210..4079276 + 67 NuclAT_39 - Antitoxin
- 4079210..4079276 + 67 NuclAT_39 - Antitoxin
- 4079210..4079276 + 67 NuclAT_41 - Antitoxin
- 4079210..4079276 + 67 NuclAT_41 - Antitoxin
- 4079210..4079276 + 67 NuclAT_41 - Antitoxin
- 4079210..4079276 + 67 NuclAT_41 - Antitoxin
- 4079210..4079276 + 67 NuclAT_43 - Antitoxin
- 4079210..4079276 + 67 NuclAT_43 - Antitoxin
- 4079210..4079276 + 67 NuclAT_43 - Antitoxin
- 4079210..4079276 + 67 NuclAT_43 - Antitoxin
FNA65_RS22215 4079590..4079697 - 108 WP_000170926.1 type I toxin-antitoxin system toxin Ldr family protein -
- 4079750..4079811 + 62 NuclAT_27 - -
- 4079750..4079811 + 62 NuclAT_27 - -
- 4079750..4079811 + 62 NuclAT_27 - -
- 4079750..4079811 + 62 NuclAT_27 - -
- 4079750..4079811 + 62 NuclAT_29 - -
- 4079750..4079811 + 62 NuclAT_29 - -
- 4079750..4079811 + 62 NuclAT_29 - -
- 4079750..4079811 + 62 NuclAT_29 - -
- 4079750..4079811 + 62 NuclAT_31 - -
- 4079750..4079811 + 62 NuclAT_31 - -
- 4079750..4079811 + 62 NuclAT_31 - -
- 4079750..4079811 + 62 NuclAT_31 - -
- 4079750..4079811 + 62 NuclAT_33 - -
- 4079750..4079811 + 62 NuclAT_33 - -
- 4079750..4079811 + 62 NuclAT_33 - -
- 4079750..4079811 + 62 NuclAT_33 - -
- 4079750..4079811 + 62 NuclAT_35 - -
- 4079750..4079811 + 62 NuclAT_35 - -
- 4079750..4079811 + 62 NuclAT_35 - -
- 4079750..4079811 + 62 NuclAT_35 - -
- 4079750..4079811 + 62 NuclAT_37 - -
- 4079750..4079811 + 62 NuclAT_37 - -
- 4079750..4079811 + 62 NuclAT_37 - -
- 4079750..4079811 + 62 NuclAT_37 - -
- 4079750..4079812 + 63 NuclAT_38 - -
- 4079750..4079812 + 63 NuclAT_38 - -
- 4079750..4079812 + 63 NuclAT_38 - -
- 4079750..4079812 + 63 NuclAT_38 - -
- 4079750..4079812 + 63 NuclAT_40 - -
- 4079750..4079812 + 63 NuclAT_40 - -
- 4079750..4079812 + 63 NuclAT_40 - -
- 4079750..4079812 + 63 NuclAT_40 - -
- 4079750..4079812 + 63 NuclAT_42 - -
- 4079750..4079812 + 63 NuclAT_42 - -
- 4079750..4079812 + 63 NuclAT_42 - -
- 4079750..4079812 + 63 NuclAT_42 - -
- 4079750..4079813 + 64 NuclAT_15 - -
- 4079750..4079813 + 64 NuclAT_15 - -
- 4079750..4079813 + 64 NuclAT_15 - -
- 4079750..4079813 + 64 NuclAT_15 - -
- 4079750..4079813 + 64 NuclAT_17 - -
- 4079750..4079813 + 64 NuclAT_17 - -
- 4079750..4079813 + 64 NuclAT_17 - -
- 4079750..4079813 + 64 NuclAT_17 - -
- 4079750..4079813 + 64 NuclAT_19 - -
- 4079750..4079813 + 64 NuclAT_19 - -
- 4079750..4079813 + 64 NuclAT_19 - -
- 4079750..4079813 + 64 NuclAT_19 - -
- 4079750..4079813 + 64 NuclAT_21 - -
- 4079750..4079813 + 64 NuclAT_21 - -
- 4079750..4079813 + 64 NuclAT_21 - -
- 4079750..4079813 + 64 NuclAT_21 - -
- 4079750..4079813 + 64 NuclAT_23 - -
- 4079750..4079813 + 64 NuclAT_23 - -
- 4079750..4079813 + 64 NuclAT_23 - -
- 4079750..4079813 + 64 NuclAT_23 - -
- 4079750..4079813 + 64 NuclAT_25 - -
- 4079750..4079813 + 64 NuclAT_25 - -
- 4079750..4079813 + 64 NuclAT_25 - -
- 4079750..4079813 + 64 NuclAT_25 - -
FNA65_RS22225 4080126..4080233 - 108 WP_000170965.1 type I toxin-antitoxin system toxin Ldr family protein -
- 4080281..4080346 + 66 NuclAT_26 - -
- 4080281..4080346 + 66 NuclAT_26 - -
- 4080281..4080346 + 66 NuclAT_26 - -
- 4080281..4080346 + 66 NuclAT_26 - -
- 4080281..4080346 + 66 NuclAT_28 - -
- 4080281..4080346 + 66 NuclAT_28 - -
- 4080281..4080346 + 66 NuclAT_28 - -
- 4080281..4080346 + 66 NuclAT_28 - -
- 4080281..4080346 + 66 NuclAT_30 - -
- 4080281..4080346 + 66 NuclAT_30 - -
- 4080281..4080346 + 66 NuclAT_30 - -
- 4080281..4080346 + 66 NuclAT_30 - -
- 4080281..4080346 + 66 NuclAT_32 - -
- 4080281..4080346 + 66 NuclAT_32 - -
- 4080281..4080346 + 66 NuclAT_32 - -
- 4080281..4080346 + 66 NuclAT_32 - -
- 4080281..4080346 + 66 NuclAT_34 - -
- 4080281..4080346 + 66 NuclAT_34 - -
- 4080281..4080346 + 66 NuclAT_34 - -
- 4080281..4080346 + 66 NuclAT_34 - -
- 4080281..4080346 + 66 NuclAT_36 - -
- 4080281..4080346 + 66 NuclAT_36 - -
- 4080281..4080346 + 66 NuclAT_36 - -
- 4080281..4080346 + 66 NuclAT_36 - -
- 4080281..4080348 + 68 NuclAT_14 - -
- 4080281..4080348 + 68 NuclAT_14 - -
- 4080281..4080348 + 68 NuclAT_14 - -
- 4080281..4080348 + 68 NuclAT_14 - -
- 4080281..4080348 + 68 NuclAT_16 - -
- 4080281..4080348 + 68 NuclAT_16 - -
- 4080281..4080348 + 68 NuclAT_16 - -
- 4080281..4080348 + 68 NuclAT_16 - -
- 4080281..4080348 + 68 NuclAT_18 - -
- 4080281..4080348 + 68 NuclAT_18 - -
- 4080281..4080348 + 68 NuclAT_18 - -
- 4080281..4080348 + 68 NuclAT_18 - -
- 4080281..4080348 + 68 NuclAT_20 - -
- 4080281..4080348 + 68 NuclAT_20 - -
- 4080281..4080348 + 68 NuclAT_20 - -
- 4080281..4080348 + 68 NuclAT_20 - -
- 4080281..4080348 + 68 NuclAT_22 - -
- 4080281..4080348 + 68 NuclAT_22 - -
- 4080281..4080348 + 68 NuclAT_22 - -
- 4080281..4080348 + 68 NuclAT_22 - -
- 4080281..4080348 + 68 NuclAT_24 - -
- 4080281..4080348 + 68 NuclAT_24 - -
- 4080281..4080348 + 68 NuclAT_24 - -
- 4080281..4080348 + 68 NuclAT_24 - -
FNA65_RS22235 4080638..4081738 - 1101 WP_001295620.1 sodium-potassium/proton antiporter ChaA -
FNA65_RS22240 4082008..4082238 + 231 WP_001146442.1 putative cation transport regulator ChaB -
FNA65_RS22245 4082396..4083091 + 696 WP_001297117.1 glutathione-specific gamma-glutamylcyclotransferase -
FNA65_RS22250 4083135..4083488 - 354 WP_001169669.1 DsrE/F sulfur relay family protein YchN -

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

Type I toxin-antitoxin system, toxin Ldr

(1-35)


Sequences

Toxin        


Download         Length: 36 a.a.        Molecular weight: 3983.80 Da        Isoelectric Point: 11.4779

>T128726 WP_000170954.1 NZ_CP041513:c4079162-4079055 [Shigella boydii]
MTLAQFAMIFWHDLAAPILAGIITAAIVGWWRNRK

Download         Length: 108 bp

>T128726 NZ_CP041513:c4079162-4079055 [Shigella boydii]
ATGACGCTCGCGCAGTTTGCCATGATTTTCTGGCACGACCTGGCAGCACCGATCCTGGCGGGAATTATTACCGCAGCGAT
TGTCGGCTGGTGGCGTAACCGGAAGTAA

Antitoxin


Download         Length: 67 bp

>AT128726 NZ_CP041513:4079210-4079276 [Shigella boydii]
GTTCTGGTTCAAGATTAGCCCCCGTTCTATTGTCAGGTTAAACCTCTCAACGTGCGGGGGTTTTCTC

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
AlphaFold DB A0A7U9LPE9

Antitoxin

Download structure file

References