Whole-genome sequencing and protease-associated functional characterization data of Bacillus amyloliquefaciens strain UzRSMMT-413 (6/4/2)
Description
This dataset contains processed whole-genome sequencing data and protease-associated bioinformatics results for Bacillus amyloliquefaciens strain UzRSMMT-413 (6/4/2), isolated from oil-contaminated sludge in Mubarak District, Kashkadarya Region, Uzbekistan. The draft genome was generated from DNBSEQ-G50 paired-end reads and consists of 29 contigs totaling 3,973,610 bp. The dataset includes read-quality reports, the curated genome assembly, QUAST, BUSCO and CheckM2 results, genome-based taxonomy using Kraken2, GTDB-Tk and TYGS, PGAP and Bakta annotations, and downstream functional analyses. Protease-associated data include MEROPS peptidase classifications, SignalP 6.0 secretion predictions, DeepTMHMM membrane-topology predictions, InterProScan domain annotations, 25 high-confidence predicted secreted peptidase-associated candidates, candidate-prioritization tables, and corresponding nucleotide and protein sequences. Additional data include CAZyme predictions, antiSMASH biosynthetic gene cluster results, AMR, CRISPR–Cas, prophage and mobile-element analyses, figure-source data, supplementary tables, metadata and reproducibility records. Raw sequencing reads are available in NCBI SRA under accession SRR41240340. The genome is deposited under WGS accession JCFFPX000000000 (version JCFFPX010000000), BioProject PRJNA1545496 and BioSample SAMN64272386.
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Raw paired-end reads were assessed with FastQC and processed with fastp. Filtered reads were assembled de novo using SPAdes v4.2.0 with the `--careful` option. Contigs shorter than 1,000 bp were removed, followed by exclusion of low-coverage contigs below 100×. The resulting 29-contig assembly was evaluated using QUAST, BUSCO and CheckM2. Taxonomic identification was performed using Kraken2, GTDB-Tk and TYGS. Genome annotation was generated using NCBI PGAP and Bakta. Functional characterization included eggNOG-mapper and InterProScan. Protease-associated analysis integrated MEROPS peptidase classification, SignalP 6.0 secretion prediction, DeepTMHMM membrane-topology prediction and Bakta/InterProScan annotations. This workflow yielded 25 high-confidence predicted secreted peptidase-associated candidates, which were subsequently reviewed and prioritized according to predicted biological role. Carbohydrate-active enzymes were analyzed using dbCAN3, and biosynthetic gene clusters were identified using antiSMASH. AMRFinderPlus, CARD/RGI, CRISPRCasFinder, PHASTEST and mobileOG-db were used for resistance- and mobile-element-related analyses. Detailed software versions, database releases, parameters, analysis provenance and recorded shell commands are provided in `01_metadata/` and Supplementary Table S1. Candidate-specific protease/peptidase classification, prioritization, and corresponding nucleotide and protein sequence files are included in the associated protease candidate dataset. Raw sequencing reads are available from NCBI SRA under SRR41240340.
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Funders
- Institute of Microbiology, Academy of Sciences of the Republic of Uzbekistan.Grant ID: N/A