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Additional file 4. Figure S4. Comparison of pheganomycin BGC locus and partly similar locus from Streptomyces viridosporus T7A. Genes are shown by block arrows, roughly to scale. Homologous genes present in both loci connected by dashed lines and the percent of identical residues is indicated in red. A table with gene annotation for both loci is shown below.

Additional file 5. Figure S5. Phylogenetic analysis of chryseoviridin precursors. Approximate maximum likelihood phylogenetic tree was built using FastTree (WAG evolutionary model, gamma distributed site rates) (Price et al. [48]). Same program was used to calculated support values, which are indicated for each branch. Four distinct branches 1 to 4 are colored by orange, green, magenta and blue respectively. Precursors from Chryseobacterium gregarium DSM 19109 are underlined.

Additional file 6. Figure S6. Phylogenetic analysis of ATP-grasps from chryseoviridin loci. Approximate maximum likelihood phylogenetic tree was built using FastTree (WAG evolutionary model, gamma distributed site rates) (Price et al. [48]). Same program was used to calculated support values, which are indicated for each branch. Two branches corresponding to two ATP-grasp proteins CdnA and CdnB encoded in chryseoviridin-like loci are indicated respectively.

Additional file 7. Figure S7. Phylogenetic analysis of flanking genes from chryseoviridin loci. A. Epimerase. B. Alpha/beta hydrolase. Approximate maximum likelihood phylogenetic trees were built using FastTree (WAG evolutionary model, gamma distributed site rates) (Price et al. [48]). Same program was used to calculated support values, which are indicated for each branch.

Additional file 2. Figure S2. Multiple alignments of selected protein families. A. Selected representatives taken from multiple alignment of precursors from cluster 2. Conserved residues in leader region are colored green, double glycine motif���blue, amino acids involved in ester and amide bonds formation���red; Underlined residues correspond to motifs of groups 8, 9 and 11 described in Lee et al. [24]. In addition, consensus sequences from Salinispora and cluster 199 aligned manually to show similarity within leader region. Abbreviations: gr8, gr9 and gr11���sequences with identified motifs of respective groups of core peptides delineated in Lee et al. [24]; ���no������sequences with no identified motifs delineated in Lee et al. [24]. B. Selected representatives taken from multiple alignment of precursors from cluster 13. Coloring is the same as in the Supplementary Figure 2A. Abbreviations: gr3, gr4, gr5 and gr6���sequences with identified motifs of respective groups of core peptides delineated in Lee et al. [24], respective motifs are underlined; ���no������sequences with no identified motifs delineated in Lee et al. [24]. The regions with a single core motif are shown by the red outline. C. Multiple alignment of LPL family of proteins. Alignments were colored using http://www.bioinformatics.org/sms2/color_align_cons.html server with default amino acid groups with 50% consensus. D. Multiple alignment of Cluster 23 and homologs. Alignments were colored using http://www.bioinformatics.org/sms2/color_align_cons.html server with default amino acid groups with 70% consensus. Residues within signal peptide region are colored cyan. Positions with conserved histidine, aspartate and asparagine marked by red letters H, D and R above the alignment. E. Multiple sequence alignment of chryseoviridin-like precursors. Alignments were colored using http://www.bioinformatics.org/sms2/color_align_cons.html server with default amino acid groups with 100% consensus. Amino acids shown experimentally to be involved in formation of lactam linkages are mapped on the CdnA3 sequence (Zhao et al., 2021).

Additional file 3. Figure S3. Diversity of precursors associated with Branch 5 ATP-grasps. The ATP_grasp subtree corresponding to branch 5 is shown. Cluster number of precursors identified in the respective ATP-grasp loci are indicated on the right.

Additional file 1. Figure S1. Identification of microviridin related BGC in two Bog Bacteria Genomes. A. Organization of microviridin related loci. MEBOG06 and MEBOG07���two Chryseobacterium sp. genomes where the loci have been identified. Coordinates of the loci indicated on the right. B. Chryseobacterium MEBOG06 and MEBOG07 microviridin precursor peptides aligned with two of the closely related precursor peptides from known Chryseobacterium genomes. Class III precursor peptides as per classification in Ahmed et al, 2017. Green���leader region motif, blue���GG motif, red���core motif as per Ahmed et al. [15] and Lee et al. [24]. 600003570, 600003571, 600003572 are microviridin precursor peptides from MEBOG06; 700001629, 700001630 are microviridin precursor peptides from MEBOG07.

The PIRSF protein classification system ( http://pir.georgetown.edu/pirsf/ ) reflects evolutionary relationships of full-length proteins and domains. The primary PIRSF classification unit is the homeomorphic family, whose members are both homologous (evolved from a common ancestor) and homeomorphic (sharing full-length sequence similarity and a common domain architecture). PIRSF families are curated systematically based on literature review and integrative sequence and functional analysis, including sequence and structure similarity, domain architecture, functional association, genome context, and phyletic pattern. The results of classification and expert annotation are summarized in PIRSF family reports with graphical viewers for taxonomic distribution, domain architecture, family hierarchy, and multiple alignment and phylogenetic tree. The PIRSF system provides a comprehensive resource for bioinformatics analysis and comparative studies of protein function and evolution. Domain or fold-based searches allow identification of evolutionarily related protein families sharing domains or structural folds. Functional convergence and functional divergence are revealed by the relationships between protein classification and curated family functions. The taxonomic distribution allows the identification of lineage-specific or broadly conserved protein families and can reveal horizontal gene transfer. Here we demonstrate, with illustrative examples, how to use the web-based PIRSF system as a tool for functional and evolutionary studies of protein families.

We examined functional and evolutionary patterns in the recently constructed set of 5,873 clusters of predicted orthologs from seven eukaryotic genomes. The analysis reveals a conserved core of largely essential eukaryotic genes as well as major diversification and innovation associated with evolution of eukaryotic genomes., Background Sequencing the genomes of multiple, taxonomically diverse eukaryotes enables in-depth comparative-genomic analysis which is expected to help in reconstructing ancestral eukaryotic genomes and major events in eukaryotic evolution and in making functional predictions for currently uncharacterized conserved genes. Results We examined functional and evolutionary patterns in the recently constructed set of 5,873 clusters of predicted orthologs (eukaryotic orthologous groups or KOGs) from seven eukaryotic genomes: Caenorhabditis elegans, Drosophila melanogaster, Homo sapiens, Arabidopsis thaliana, Saccharomyces cerevisiae, Schizosaccharomyces pombe and Encephalitozoon cuniculi. Conservation of KOGs through the phyletic range of eukaryotes strongly correlates with their functions and with the effect of gene knockout on the organism's viability. The approximately 40% of KOGs that are represented in six or seven species are enriched in proteins responsible for housekeeping functions, particularly translation and RNA processing. These conserved KOGs are often essential for survival and might approximate the minimal set of essential eukaryotic genes. The 131 single-member, pan-eukaryotic KOGs we identified were examined in detail. For around 20 that remained uncharacterized, functions were predicted by in-depth sequence analysis and examination of genomic context. Nearly all these proteins are subunits of known or predicted multiprotein complexes, in agreement with the balance hypothesis of evolution of gene copy number. Other KOGs show a variety of phyletic patterns, which points to major contributions of lineage-specific gene loss and the 'invention' of genes new to eukaryotic evolution. Examination of the sets of KOGs lost in individual lineages reveals co-elimination of functionally connected genes. Parsimonious scenarios of eukaryotic genome evolution and gene sets for ancestral eukaryotic forms were reconstructed. The gene set of the last common ancestor of the crown group consists of 3,413 KOGs and largely includes proteins involved in genome replication and expression, and central metabolism. Only 44% of the KOGs, mostly from the reconstructed gene set of the last common ancestor of the crown group, have detectable homologs in prokaryotes; the remainder apparently evolved via duplication with divergence and invention of new genes. Conclusions The KOG analysis reveals a conserved core of largely essential eukaryotic genes as well as major diversification and innovation associated with evolution of eukaryotic genomes. The results provide quantitative support for major trends of eukaryotic evolution noticed previously at the qualitative level and a basis for detailed reconstruction of evolution of eukaryotic genomes and biology of ancestral forms.

Background The availability of multiple, essentially complete genome sequences of prokaryotes and eukaryotes spurred both the demand and the opportunity for the construction of an evolutionary classification of genes from these genomes. Such a classification system based on orthologous relationships between genes appears to be a natural framework for comparative genomics and should facilitate both functional annotation of genomes and large-scale evolutionary studies. Results We describe here a major update of the previously developed system for delineation of Clusters of Orthologous Groups of proteins (COGs) from the sequenced genomes of prokaryotes and unicellular eukaryotes and the construction of clusters of predicted orthologs for 7 eukaryotic genomes, which we named KOGs after eukaryotic orthologous groups. The COG collection currently consists of 138,458 proteins, which form 4873 COGs and comprise 75% of the 185,505 (predicted) proteins encoded in 66 genomes of unicellular organisms. The eukaryotic orthologous groups (KOGs) include proteins from 7 eukaryotic genomes: three animals (the nematode Caenorhabditis elegans, the fruit fly Drosophila melanogaster and Homo sapiens), one plant, Arabidopsis thaliana, two fungi (Saccharomyces cerevisiae and Schizosaccharomyces pombe), and the intracellular microsporidian parasite Encephalitozoon cuniculi. The current KOG set consists of 4852 clusters of orthologs, which include 59,838 proteins, or ~54% of the analyzed eukaryotic 110,655 gene products. Compared to the coverage of the prokaryotic genomes with COGs, a considerably smaller fraction of eukaryotic genes could be included into the KOGs; addition of new eukaryotic genomes is expected to result in substantial increase in the coverage of eukaryotic genomes with KOGs. Examination of the phyletic patterns of KOGs reveals a conserved core represented in all analyzed species and consisting of ~20% of the KOG set. This conserved portion of the KOG set is much greater than the ubiquitous portion of the COG set (~1% of the COGs). In part, this difference is probably due to the small number of included eukaryotic genomes, but it could also reflect the relative compactness of eukaryotes as a clade and the greater evolutionary stability of eukaryotic genomes. Conclusion The updated collection of orthologous protein sets for prokaryotes and eukaryotes is expected to be a useful platform for functional annotation of newly sequenced genomes, including those of complex eukaryotes, and genome-wide evolutionary studies.