This folder contains the genomic analyses of candidate superproducer lineages to identify candidate RBPs, which we want to use to facilitate their isolations.

The directory is organised as follows:
├── acidobacteriota/ --> Folder containing the genomic analysis of acidobacteriota candidate superproducer lineages
    ├── environmental-genomes/ --> Folder containing the newly reconstructed species through environmental genomics
    └── isolates/ --> Folder containing the two isolates
        ├── acanthopleuribacter-pedis/ --> Analyses for the first isolate, Acanthopleuribacter pedis
        └── sulfidibacter-corallicola/ --> Analyses for the second isolate, Sulfidibacter corallicola
└── other/ --> Folder containing the genomic analysis of other candidate superproducer lineages (including Alphaproteobateria, Cyanobacteria, Desulfobacteria, etc)
    └── environmental-genomes/ --> These are only represented by environmental genomes 

For every genome, the folder is organised as follows:
├── genome.fa --> genomic information in fasta format 
├── genome.genes.faa --> all the proteins
├── genome-PhageRBPpredictions-all.tsv --> Positive PhageRBPpredictions across the whole genome
├── genome-PhageRBPpredictions-all.faa --> Sequences of the potential RBPs 
├── genome-PhageRBPpredictions-trimer-structures --> If appropriate, trimer predicted structures of select RBP candidates 
├── genome-genomad-summary.tsv --> Summary of the GeNomad results
├── genome-genomad-prophage_*.fna --> genomic information of the prophage in fasta format 
├── genome-genomad-prophage_*-proteins.faa --> proteins of the prophage in fasta format 
├── genome-genomad-prophage_*-proteins.list --> list of proteins in the prophage 
├── genome-genomad-prophage_*-annotations.tsv --> annotations of the prophage's proteins 
├── genome-genomad-prophage_*-proteins.map --> map between the proteins in the prophage and in the genome (they have different names). This excludes partial CDS. 
├── genome-genomad-prophage_*-PhageRBPpredictions.tsv --> PhageRBPpredictions for the prophage's proteins 
├── genome-phaster-summary.txt --> Summary of the phaster results (if applicable) 
├── genome-phaster-detail.txt --> Detailed phaster results 
├── genome-phaster-output.html --> Link to the interactive phaster results 
├── genome-phaster-prophage_*-genomic.fna --> genomic information of the prophage in fasta format 
├── genome-phaster-prophage_*-proteins.faa --> proteins of the prophage in fasta format 
├── genome-phaster-prophage_*-proteins.map --> map between the proteins in the prophage and in the genome (they have different names). This excludes partial CDS. 
└── genome-phaster-prophage_*-PhageRBPpredictions.tsv --> PhageRBPpredictions for the prophage's proteins