Datasets for Lupo et al. (2022) Origin and Evolution of Pseudomurein Biosynthetic Gene Clusters

Lupo et al. 2022 Pseudomurein: Archive content for v1 Overview ... 61 directories, 769 files README.md: this file. command-line.sh: examples of bash commands to use or generate the files stored in this archive. 10-archaeal-proteomes This directory contains an archive (.tar.gz) consisting of FASTA (.faa) files of the 10 organisms used by OrthoFinder. alphafold List of ZIP (.zip) files containing the raw results of AlphaFold predictions and Consurf results. archaeal-genomes This directory contains an archive (.tar.gz) consisting of 819 FASTA (.faa) files corresponding to the archaeal database. bacterial-genomes This directory contains an archive (.tar.gz) consisting of 598 FASTA (.faa) files corresponding to the bacterial database. config This directory contains two configuration files (.yaml) used by the classify-ali.pl perl script from Bio::MUST modules: classifier.yaml is the configuration file used to filter the 6,321 orthologous groups (OGs). five_org_classifier.yaml is the configuration file used to filter the OGs after the round of Forty-Two TBLASTN. BLASTP List of configuration files to run Forty-Two BLASTP (FILTERING OF CANDIDATE PROTEINS; see figure S1 in the main manuscript). TBLASTN List of configuration files to run Forty-Two TBLASTN (FILTERING OF CANDIDATE PROTEINS; see figure S1 in the main manuscript). NCBI_CCD List of HMM (.hmm) profile files downloaded from NCBI CDD database and corresponding HMM search (.hmms) files. ompapa-results Raw Ompa-Pa results associated with NCBI CDD HMM profiles. ompapa This directory contains a list of the OGs that have passed the taxonomic filter (see config sections). alignments List of alignments in FASTA format of the OGs included in the retained_OGs.lis file (see ompapa section). bacterial_db Results of ompapa analyses against the bacterial database. This directory contains two sub-directories: hmms that contains a list of HMM search (.hmms) files. ompapa-results that contains raw ompapa results. hmm_profiles List of HMM (.hmm) profiles of the OGs included in the retained_OGs.lis file (see ompapa section). prokaryotic_db Results of ompapa analyses against the prokaryotic database. This directory contains two sub-directories: hmms that contains a list of HMM search (.hmms) files. ompapa-results that contains raw ompapa results. orthologous-groups This directory contains an archive (.tar.gz) consisting of 6,321 FASTA (.fasta) files corresponding to the OGs generated by OrthoFinder. predictions This directory contains three sub-directories: interproscan that contains raw InterProScan results. signalp5 that contains raw SignalP5 results. tmhmm that contains raw TMHMM results. For the consolidated results, see Table S1 in the main manuscript. prokaryotic-genomes This directory contains a list of assembly accessions of the 80,490 organisms from the prokaryotic database. regulon This directory contains all the data needed to reproduce the ‘regulon pipeline’ (see supplementary data from the main manuscript). All the command lines are included in the command_line_regulon.sh file. scripts This directory contains various perl scripts used to generate some of the files stored in this archive (see command-line.sh file). taxdump Mirror of the NCBI Taxonomy used in this study (downloaded on 4th of May 2020). trees This directory contains three sub-directories: atp-grasp mray-family mur-family All the sub-directories contains tree (.tre) files presented in the main manuscript and corresponding raw IQ-TREE (.ckp.gz) results. They also contain various files needed to reproduce the phylogenetic analyses (see command-line.sh file).