Detailed information of TA system    

insolicoBioinformatically predicted

Overview

TA module


Type II Classification (family/domain) vapBC/VapC-StbC
Location 506137..506816 Replicon chromosome
Accession NC_009636
Organism Sinorhizobium medicae WSM419

Toxin (Protein)


Gene name vapC Uniprot ID A0A508X4J2
Locus tag SMED_RS02350 Protein ID WP_011974672.1
Coordinates 506391..506816 (+) Length 142 a.a.

Antitoxin (Protein)


Gene name vapB Uniprot ID A6U6P5
Locus tag SMED_RS02345 Protein ID WP_011974671.1
Coordinates 506137..506394 (+) Length 86 a.a.

Genomic Context

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
SMED_RS02330 501166..503100 + 1935 WP_011974668.1 DUF2207 domain-containing protein -
SMED_RS02335 503291..505456 + 2166 WP_011974669.1 glycine--tRNA ligase subunit beta -
SMED_RS02340 505520..506005 + 486 WP_011974670.1 DUF523 domain-containing protein -
SMED_RS02345 506137..506394 + 258 WP_011974671.1 Arc family DNA-binding protein Antitoxin
SMED_RS02350 506391..506816 + 426 WP_011974672.1 type II toxin-antitoxin system VapC family toxin Toxin
SMED_RS02355 506977..507483 - 507 WP_011974673.1 hypothetical protein -
SMED_RS02360 507600..508871 - 1272 WP_011974674.1 phosphoribosylamine--glycine ligase -
SMED_RS02365 508946..511316 - 2371 Protein_469 bifunctional diguanylate cyclase/phosphodiesterase -

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

(2-122)

Antitoxin

Arc-like DNA binding domain

(9-46)


Sequences

Toxin        


Download         Length: 142 a.a.        Molecular weight: 15354.81 Da        Isoelectric Point: 8.4587

>T22260 WP_011974672.1 NC_009636:506391-506816 [Sinorhizobium medicae WSM419]
VIVLDTNVISELWRIEPDSNVLTWIDAQMVETLYLSTITVAELRFGLAAMPAGTRRTIYLDRLEREVLPAFSGRVLPFDL
GASQAYANLMARVKMAGRGIGKADGYIAATAASRGLMVATRDVSPFEAAGLTVLNPWRAAR

Download         Length: 426 bp

>T22260 NC_009636:506391-506816 [Sinorhizobium medicae WSM419]
GTGATCGTTCTCGATACCAACGTGATCTCCGAACTGTGGAGGATCGAGCCGGATTCCAACGTGCTGACCTGGATCGACGC
GCAGATGGTGGAAACCCTCTACCTGTCCACGATCACGGTAGCCGAACTGCGCTTCGGTTTAGCGGCCATGCCCGCAGGCA
CGCGTCGAACGATCTATTTGGATCGGTTGGAGCGAGAGGTCTTGCCGGCCTTTTCCGGGCGTGTCCTGCCCTTCGATCTG
GGCGCCTCACAGGCCTATGCTAACCTGATGGCGCGGGTGAAAATGGCTGGCAGGGGCATCGGAAAGGCGGACGGCTACAT
CGCCGCGACGGCGGCATCACGCGGCCTGATGGTTGCCACTCGAGATGTCAGTCCATTCGAGGCGGCAGGACTGACCGTCC
TTAACCCCTGGCGCGCCGCGCGATGA

Antitoxin


Download         Length: 86 a.a.        Molecular weight: 9202.47 Da        Isoelectric Point: 6.4625

>AT22260 WP_011974671.1 NC_009636:506137-506394 [Sinorhizobium medicae WSM419]
MPSITIRNVPSEVHRAIRVRAAMHGCSTEAEIRSILEQAAKPEGRLKLGSLLTSIAREAGGLTDSEAEGFNQLRDKTPAE
PMGFE

Download         Length: 258 bp

>AT22260 NC_009636:506137-506394 [Sinorhizobium medicae WSM419]
ATGCCATCAATCACAATCCGCAACGTTCCGAGCGAGGTGCATCGTGCTATCCGTGTTCGGGCGGCCATGCACGGCTGTAG
CACCGAGGCCGAAATTCGCAGCATCCTCGAACAGGCCGCCAAGCCCGAGGGTCGCTTGAAGCTTGGTTCACTGCTGACGT
CAATTGCGCGCGAAGCGGGGGGGCTGACCGACTCCGAAGCCGAGGGCTTCAATCAGCTTCGCGACAAGACCCCGGCCGAG
CCGATGGGCTTTGAGTGA

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 A0A508X4J2

Antitoxin

Source ID Structure
AlphaFold DB A6U6P5

References