LPSN is a free to use service founded by Jean P. Euzby in 1997 and later on maintained by Aidan C. Parte. When referring to information from the LPSN web interface, cite: When using the LPSN Application Programming Interface (API), cite: When citing LPSN always mention the date on which you accessed the website or the API. Otherwise, it is provided with the species name. PNU had been established in 1993 as a service of the Leibniz Institute DSMZ, and was curated by Norbert Weiss, Manfred Kracht and Dorothea Gleim. ], Truper, H.G., "Taxonomic notes: Names for higher taxa and their impact on the Code of Nomenclature of Bacteria." 2022-09-22 The advanced search can filter for the nomenclatural status and for the "proposed as" entries. The search can also be refined by specifying (i) the full name (or part of the name) of a metabolic pathway or a functional feature (e.g. Taxonomy of Bacteria | Organisms | Microbiology. (1994) 44:338-347. Progress in genome sequencing and bioinformatics opens up new possibilities, including that of correlating genome annotations with functional information such as metabolic pathways. The authors are grateful to Gail Wagman for her correction of the English-language version. PATRIC depends on the KEGG pathway data and cannot be downloaded (Table 1). These PS and PFS data are useful to biologists for data mining. First, the user has the possibility to explore functional traits at different taxonomic levels, from phyla to species, or dedicated strains covering both the Archaea and Bacteria kingdoms. Bacteriol. Its advantages are 4-fold. "Report of the ad hoc committee for the re-evaluation of the species definition in bacteriology." Otherwise, the user has to query on all ranks. . For many years, Bergeys Manual of Determinative Bacteriology (1) and its successor, Bergeys Manual of Systematic Bacteriology (26), which provides descriptions of the taxonomy, systematics, ecology, physiology and other biological properties of all described prokaryotic taxa, has been the best consensus for an official prokaryotic classification and the best source of information for prokaryotic organisms and taxa. French National Institute for Agricultural Research (PHASE division); Region Occitanie (R9090198/00100870 to M.L.B.). Bacteriol. We present MetAboliC pAthways DAtabase for Microbial taxonomic groups (MACADAM) here, a user-friendly database that makes it possible to find presence/absence/completeness statistics for metabolic pathways at a given microbial taxonomic position. Bacteriol. "A multiple-outgroup approach to resolving division-level phylogenetic relationships using 16S rDNA data." Read more. The SILVA taxonomy is mostly a secondary data resource that integrates information from several external resources of nomenclature and classification. Bacterial taxonomy is studied to provide adequate information on identity and uniqueness of a species in their ecological, clinical, and industrial niche environments. For example, E. coli is described as Bacteria, Proteobacteria, Gammaproteobacteria, Enterobacterales, Enterobacteriaceae, and Escherichia. In the latter case, the pathway is still present because of the functional inference applied by MetaCyc experts, information that they cross-reference with phenotypic evidence described in the literature. Since the source code to build MACADAM is available to everyone (GitHub URL: https://github.com/maloleboulch/MACADAM-Database), MACADAM can be included in any functional inference tool able to integrate the abundance tables of complete microbial communities generated, among others, we plan to include MACADAM in the FROGS software (39) to analyze amplicon metagenomics data. Int. MACADAM contains eight pathways in 1519 organisms with a PS equal to 0. By comparing the PS and PFS in A and B, pathway A shows greater evidence of its veracity. HMDB, Reactome and WikiPathways are manually and highly curated, but, despite the high quality of their functional information, they cover a small number of organisms [1, 1 and 31 (3 of which are microbes), respectively]. For each organism encoded with its taxID key, the FAPROTAX table and the IJSEMPhenoDB table contain its numeric lineage (taxonomy key) and complementary information such as functional features (pathwayName or pathway keys), environmental habitat or substrate to culture the organism. (, Karp, P.D., Weaver, D., Paley, S. et al. [1] The journal Nucleic Acids Research regularly publishes special issues on biological databases and has a list of such databases. Palys, T., Nakamura, L.K., and Cohan, F.M. Furthermore, the bacterial code of . The Genome Taxonomy Database (GTDB) is an initiative to establish a standardised microbial taxonomy based on genome phylogeny, primarily funded by the Australian Research Council via a Laureate Fellowship (FL150100038) and Discovery Project (DP220100900), with the welcome assistance of strategic funding from The University of Queensland. MACADAM contains a total of 7921 metabolites, 592 enzymatic reactions, 2134 EC numbers and 7440 enzymes. Taxonomy is an organizing principle of biology and is ideally based on evolutionary relationships among organisms. Hansmann, S., and Martin, W. "Phylogeny of 33 ribosomal and six other proteins encoded in an ancient gene cluster that is conserved across prokaryotic genomes: influence of excluding poorly alignable sites from analysis." MACADAM can be explored via metabolites, reactions, enzymes, EC numbers or specific pathways. Information from sequence entries Show organism modifiers. Examples of output files corresponding to requests on MACADAM. Microbiol. et al. Bacterial taxonomy & classification Dr. Mohammedazim Bagban B.Sc. Thanks to the development of functional annotation databases, scientists are able to link genome annotations with functional annotations. designed to assist medical and public health laboratory personnel located anywhere in the world in identifying bacterial and fungal pathogens. (in: Bacteria). (1994) 368-369. The science in which the bacteria are classified is called bacterial taxonomy. (1987) 9:34-39. WikiPathways does not appear in Table 1 because it contains only three microbial organisms and it is not useful for microbial queries. Christensen, H., Bisgaard, M., Frederiksen, W., Mutters, R., Kuhnert, P., and Olsen, J.E. Tools. Each MACADAM organism is therefore associated with its numeric lineage formed by seven taxID. The genomes used to construct the phylogeny are . Find diseases associated with this biological target and compounds tested against it in bioassay experiments. What is a disadvantage of setting the taxonomy to E. coli. Each rank and organism is described by its NCBI taxID. As for FAPROTAX, it indicates functional information described in the literature at the genus rank if all described species of the genus have been shown to exhibit the given functional information and not the addition of functional information about all of the organisms belonging to this rank. a total of 1656 PGDBs (1560 bacteria and 96 archaea). Database (Oxford). GTDB-Tk is a software toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes based on the Genome Database Taxonomy . (2001) 51:667-678. Evol. PATRIC (11) is a bacterial database containing >201000 prokaryotic genomes, each associated with functional information. A high proportion shows a high presence of targeted pathways among targeted taxonomic names. The UBCG app allows an easy, fast and very accurate way to determine phylogenomic relationships between strains, making the previously hard work of phylogenomics an easy task, even if you are not an expert in bioinformatics. (eds) (, Kanehisa, M., Furumichi, M., Tanabe, M. et al. "Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya." "Suggestions for avoiding on-going confusion from the Bacteriological Code." "Is characterization of a single isolate sufficient for valid publication of a new genus or species? The Genome Taxonomy Database (GTDB) is an initiative to establish a standardised microbial taxonomy based on genome phylogeny. Pannonibacter phragmitetus C6/19 is a facultative anaerobe, Microbiol. et al. Microbiol. Data is also accessible through public MySQL databases and our FTP site containing full data dumps in FASTA, EMBL, GTF, GFF3, JSON and RDF formats. MACADAM functional diversity for phyla with >10 PGDBs in MACADA (A) among bacterial phyla, (B) among archaea phyla, (C) the 10 main hierarchical groups of pathways in all bacterial organisms and (D) the 10 main hierarchical groups of pathways in all archaea organisms. Euzby, J.P. (1997). they associate the genome sequences with metabolic pathways. All. PSs range from 0 to 1 (Table 2). GENOME TAXONOMY DATABASE. In addition, 118 bacteria are labeled reference genome (no archaea). The EPPO Global Database ( https://gd.eppo.int/) provides relevant information on these phytobacteria such as their geographical distribution, host plant, symptomatology and detection protocols. MACADAM contains a total of 7921 metabolites, 592 enzymatic reactions, 2134 EC numbers and 7440 enzymes. "Relationship of 16S rRNA sequence similarity to DNA hybridization in prokaryotes." The informal name "bacteria" is occasionally used loosely in the literature to refer to all of the prokayrotes, and care should be taken to interpret it's meaning in any particular context. Appl. The taxonomy is the combination of two words that is taxis means arrangement and nomos means to distribute or govern. MicroCyc is a collection of PGDBs created within the framework of the MicroScope project (29) based on MetaCyc data. We thus build a PGDB per organism, i.e. a whole family). (, Caspi, R., Billington, R., Fulcher, C.A. chemoorganotroph, mesophilic bacterium that forms circular colonies and was isolated from surface of decomposing reed rhizomes. Thus, for common PGDBs between the two databases, those from MicroCyc are chosen over those from MetaCyc and are included in MACADAM, i.e. J. Syst. Each reaction can be described by its name, its metabolites, its enzymes and its EC numbers. Therefore, if the organism contains this reaction, the whole pathway will be identified for the organism. J. Syst. (A) The user has searched for all metabolic pathways in S. aureus and K. aureofaciens, using the term urea in the function field text. series of chemical reactions catalyzed by enzymes within a cell. Data is also accessible through public MySQL databases and our FTP site containing full data dumps in FASTA, EMBL, GTF, GFF3, JSON and RDF formats. J. Syst. Int. J. Syst. Since this information has a different structure, the PS cannot be calculated. The taxonomy database provides more than two million species information retrieval. Who: MACADAM database benefits from the GenoToul Bioinformatics Platform facilities, including a permanent staff and technical support. Since there is no data on this organism in MACADAM, the information was searched for higher up in the taxonomy hierarchy, i.e. Murray, R.G., and Schleifer, K.H. To make this possible, databases have been built and contain metabolic pathways, e.g. The current release of CLARK-S exploits discriminative spaced k-mers (see the peer-reviewed publication).The classification can be done, like CLARK or CLARK-l, at phylum, genus or species level for example.Before classifying your metagenomic sample, you must first create the database of discriminative 31-mers (e.g., bacteria/archaea genomes) and then databases of discriminative spaced 31-mers . With existing databases, it is difficult to request up-to-date functional annotations and up-to-date taxonomic lineages for a taxon (e.g. See more details about this update in our blog. Currently, among available databases, some databases are highly curated, including the EcoCyc (13), BsubCyc (14) and HumanCyc (15) databases devoted to Escherichia coli K-12, Bacillus subtilis or human metabolic pathways, respectively. the new dashboard enables to explore BacDive The Genome Taxonomy Database (GTDB) is an initiative to establish a standardised microbial taxonomy based on genome phylogeny, primarily funded by the Australian Research Council via a Laureate Fellowship (FL150100038) and Discovery Project (DP220100900), with the welcome assistance of strategic funding from The University of Queensland.. Acad. (1997) 47:590-592. Ensembl Bacteria release 55 - Oct 2022 Data resources update Help. However, to provide users with functional information at these upper ranks, MACADAM needs to store all prokaryotic taxonomies. Bacteriol. ], Tindall, B.J. subclasses or subgenera, these minor ranks are kept in MACADAM so that users can find functional information at these minor ranks. In fact, butyrate is a microbial fermentation product that is used as an energy source by enterocytes and whose signaling properties are involved in multiple functions of enterocytes, including cell differentiation, gut tissue development, immune modulation, oxidative stress reduction and diarrhea control (38). Forum. J. Syst. (, Escudi, F., Auer, L., Bernard, M. et al. The genomes used to construct the phylogeny are obtained . . J. Syst. [2] NCBI Taxonomy: a comprehensive update on curation, resources and tools. Int. . SILVA, RDP, Greengenes, NCBI and OTThow do these taxonomies compare? The taxonomic name "Bacteria" refers only to the eubacteria. Moore, L.V., Bourne, D.M., and Moore, W.E. Int. Thanks to the column that gives the number of organisms with the targeted pathway (column 2 in Figure 6B), it is possible to see pathways that are more or less conserved in the taxon of interest. Genome sequencing facilitates the study of bacterial taxonomy and allows the re-evaluation of the taxonomic relationships between species. "Misunderstanding the Bacteriological Code." MACADAM is not intended to replace existing databases but provides additional information for scientists wishing to better characterize the functional information of all taxonomic groups, from phyla to species. Statistics on the L-lysine fermentation to acetate and butanoate pathway (MetaCyc ID is P163-PWY; values in brackets are minimum and maximum values. (, Louca, S., Parfrey, L.W. "Proposal to change the Rule governing the designation of type strains deposited under culture collection numbers allocated for patent purposes." the rank -based classification, of bacteria . Malo Le Boulch, Patrice Dhais, Sylvie Combes, Graldine Pascal, The MACADAM database: a MetAboliC pAthways DAtabase for Microbial taxonomic groups for mining potential metabolic capacities of archaeal and bacterial taxonomic groups, Database, Volume 2019, 2019, baz049, https://doi.org/10.1093/database/baz049. 49 different graphs within seven sections give a fast overview of the data provided in the database including . Comparison of PS of all metabolic pathways of PGDBs present in both MetaCyc PGDBs and MicroCyc PGDBs. Microbiol. Int. An important feature of MACADAM is its ability to infer functional annotations for taxa with no associated genomic sequences using the taxonomy. relevant scientific literature for the most reliable information. (2001) 51:385-391. For example, if a species has no functional information, MACADAM automatically requests functional information at the genus level, just like FAPROTAX. The fourth key is the numberOfPGDBInSpecies. MACADAM will be useful to all biologists who need to determine the functional potential of a prokaryotic species or any other taxonomic rank. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (, PharmaKoVariome database for supporting genetic testing, BRACS: A Dataset for BReAst Carcinoma Subtyping in H&E Histology Images, Assigning species information to corresponding genes by a sequence labeling framework, KinMod database: a tool for investigating metabolic regulation, Ontology Development Kit: a toolkit for building, maintaining and standardizing biomedical ontologies, About the International Society for Biocuration, MACADAM: main characteristics and added value, https://github.com/maloleboulch/MACADAM-Database, https://ijs.microbiologyresearch.org/content/journal/ijsem, http://creativecommons.org/licenses/by/4.0/, Receive exclusive offers and updates from Oxford Academic, On one or several taxonomies or organisms, with few filters, On one or several taxonomies or organisms, with multiple filters, RefSeq (functional annotations), MetaCyc (metabolic pathways), MicroCyc (metabolic pathways), FAPROTAX (functional features), IJSME PhenoDB (phenotypic data), Genbank/RefSeq (annotations) and MetaCyc (metabolic pathways), Genbank/RefSeq, KEGG (metabolic pathways), SmartTables, genome browser, omics data analysis, metabolic models and routes and comparative analysis, KEGG pathway map, comparative pathway heatmap, multiple sequence alignment, enzymes and genes conservation in pathway, Metabolic pathway name, pathway class hierarchy, hyperlink to MetaCyc pathway and functional information of the upper rank for taxa without data, Metabolic pathway name, pathway class hierarchy, pathway map including enzymes and metabolites, associated genes, protein associated with pathways and literature references, Metabolic pathway name, pathway class hierarchy, KEGG pathway map including enzymes and metabolites, associated genes, enzyme and gene evolution data, Metabolic pathway name, pathway class hierarchy, KEGG pathway map including enzymes and metabolites, associated genes and literature references, MicroCyc PGDBs that have replaced a MetaCyc PGDB, Number of reactions in the complete pathway, Number of bacteria in which this pathway is present, Median number of unique enzymes present in this pathway in organisms, Median number of enzymes present in this pathway in organisms. The taxonomic name "Bacteria" refers only to the eubacteria. "A phylogenetic definition of the major eubacterial taxa." Bacteriol. Moreover, to ensure up-to-date annotations, we compute PGDBs with Pathway Tools at each release, based on RefSeq, NCBI taxonomy, MetaCyc, MicroCyc, FAPROTAX and the IJSEM phenotypic database. To access Ensembl Genomes data from any programming language, try our REST service. 2020: baaa062. The second one is the ID key that is a unique identifier associated with each PGDB. A standardized score enables quick comparison and comprehension of the potential presence of a pathway. Ensembl Genomes is developed by EMBL-EBI and is powered by the Ensembl software system for the analysis and visualisation of genomic data. Viale, A.M., Arakaki, A.K., Soncini, F.C., and Ferreyra, R.G. "Comparative distribution and taxonomic value of cellular fatty acids in thirty-three genera of anaerobic gram-negative bacilli." For a representative overview, data can be Int. A user-friendly web interface makes querying easy. Jr, Bult, C., and Fields, C. "Intraspecific variation in small-subunit rRNA sequences in GenBank: why single sequences may not adequately represent prokaryotic taxa." Syst. (2000) 50:1655-1663. Entrez PubMed Nucleotide Protein Genome Structure PMC Taxonomy BioCollections Search for as complete name wild card token set phonetic name taxonomy idlock levels using filter: Tindall, B.J. The generation of the unique ID and the calculation of the PS take around 6h each due to file movements and extraction of archives. Therefore, I'd like to add some sequences whose prefix are "NZ_" to the custom database. J. Syst. Groups of this rank or level unite creating a group of higher rank or level. Search for other works by this author on: Sigenae Group, GenPhySE, Universit de Toulouse, INRA, INPT, ENVT, Castanet Tolosan, France. (, Wattam, A.R., Davis, J.J., Assaf, R. et al. List of Bacterial Names with Standing in Nomenclature: a Folder Available on the Internet. We therefore obtain an improved set of PGDBs from MetaCyc and MicroCyc, completed with functional annotations of 13509 organisms (Table 1). (eds) (, Wadi, L., Meyer, M., Weiser, J. et al. Euzeby, J.P. "List of Bacterial Names with Standing in Nomenclature: a folder available on the Internet." Impact of outdated gene annotations on pathway enrichment analysis, The ecology of acidobacteria: moving beyond genes and genomes, Production of butyrate from lysine and the Amadori product fructoselysine by a human gut commensal, FROGS: Find, Rapidly, OTUs with Galaxy Solution. To ensure high-quality genomic data, we only kept the 11794 organisms (11514 bacteria and 280 archaea) with complete genome RefSeq labels (Table 2). (1894) I.G. Instead, microbiologists have been forced to use hard-to-remember alphanumeric placeholder . (1999) 49:1317-1319. b. Using the standardized pathway score (PS; Figure 2) proposed in Pathway Tools 16.5, we compare MetaCyc and MicroCyc PGDBs for each organism that is present in both databases. Browsers. [No abstract available. Currently, this rank is assigned to 167 bacterial and 39 archaeal informal names in NCBI Taxonomy. 317,542 genomes. FAPROTAX (18) or the IJSEM phenotypic database (19, 20). Overview of MACADAM, BioCyc, PATRIC and KEGG database features with a focus on metabolic pathway and functional information among prokaryotic organisms. Of course, several studies demonstrated the 16S ribosomal RNA could be considered as a barcode for bacteria classification at the genus level, but till now it is hard to identify the correct composition of metagenomic data from RNA-seq short-read data. ], Translation table 11 (Bacterial, Archaeal and Plant Plastid), Immune Epitope Database and Analysis Resource. The file also contains the names of the organisms in which the pathways are found and the metabolic hierarchy associated with the pathways. (2000) 50:1687-1689. The reasons are either that the pathway is from MicroCyc, that the pathway has a high enough threshold quality score, or that the metabolic pathway is complete. (, Sayers, E.W., Barrett, T., Benson, D.A. [No PubMed record available.]. Parte, A.C. (2014). There are several models of the branching order of bacterial phyla, one of these is the Genome Taxonomy Database (GTDB). It furthers the University's objective of excellence in research, scholarship, and education by publishing worldwide, This PDF is available to Subscribers Only. Briefly, in MACADAM, each organism taxonomy has seven taxonomic ranks: superkingdom, phylum, class, order, family, genus and species. MACADAM can be queried at any rank of the NCBI taxonomy (from phyla to species). (1999) 49:1321-1322. The database file (SQLite format) with a query script is downloadable at http://macadam.toulouse.inra.fr. Second, MACADAM relies on up-to-date NCBI taxonomy (2224). Note: species that already exist on this site will continue to be updated with the full range of annotations. SILVA maintains a taxonomic resource for the SSU and LSU rRNA sequences of Bacteria, Archaea and Eukarya that are gathered from public nucleic acid sequence repositories. If the more general class of bacteria were chosen a homologous protein from a different bacteria could be . Reference: How to cite this resource - Schoch CL, et al. A: among Bacteria; B: among Archaea. The second column provides the number of organisms that have the targeted pathway. (, Altman, T., Travers, M., Kothari, A. et al. (, Vallenet, D., Labarre, L., Rouy, Z. et al. In the case of a taxon with no functional information in MACADAM, i.e. Int. (, Kielak, A.M., Barreto, C.C., Kowalchuk, G.A. Reliable data are needed to infer the functional potential of complex prokaryotic communities. Python CGI is used for the frontend web interface. Although. Biotech Biochem II BM Unit-1.2 Taxonomy and Classification Rai University Bergey's manual of bacterial classification nj1992 Advertisement More Related Content Slideshows for you (17) Introduction to Modern Biosystemaics for Fungal Classification Mrinal Vashisth Microbial taxonomy To link this information, we connected data from PGDBs, the FAPROTAX and the IJSEM phenotypic database with their NCBI taxonomy ID (taxID). The last columns contain targeted taxonomy names, the list of strains that have the pathways and the MetaCyc metabolic pathway hierarchy with the corresponding URL. et al. "A definition of the domains Archaea, Bacteria and Eucarya in terms of small subunit ribosomal RNA characteristics." (LPSN; http://www.bacterio.net/) and the 10 other newly proposed phyla from the NCBI taxonomy (Figure 7). Contribute; Taxonomic Workbench Help : Welcome to ITIS, the Integrated Taxonomic Information System! : +33 (0)5 61 28 51 05; Fax: +33 (0)5 61 28 53 19; Email: KEGG: new perspectives on genomes, pathways, diseases and drugs, HMDB 4.0: the Human Metabolome Database for 2018, WikiPathways: a multifaceted pathway database bridging metabolomics to other omics research, Improvements to PATRIC, the all-bacterial bioinformatics database and analysis resource center, The BioCyc collection of microbial genomes and metabolic pathways, The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases, Computational prediction of human metabolic pathways from the complete human genome, The MetaCyc database of metabolic pathways and enzymes, MicroScope in 2017: an expanding and evolving integrated resource for community expertise of microbial genomes, Decoupling function and taxonomy in the global ocean microbiome, Hiding in plain sight: mining bacterial species records for phenotypic trait information, A systematic comparison of the MetaCyc and KEGG pathway databases, Database resources of the National Center for Biotechnology Information, RefSeq microbial genomes database: new representation and annotation strategy, NCBI Reference Sequences (RefSeq): current status, new features and genome annotation policy, NCBI prokaryotic genome annotation pipeline, Pathway Tools version 19.0 update: software for pathway/genome informatics and systems biology, MicroScope: a platform for microbial genome annotation and comparative genomics, Enzyme-specific profiles for genome annotation: PRIAM, MaGe: a microbial genome annotation system supported by synteny results. All these databases are referred to as pathway genome databases (PGDBs); i.e. Database Files; Download Data in TWB Format; Become a Data Partner. "Discovery and classification of ecological diversity in the bacterial world: the role of DNA sequence data." [No abstract available. Statistics on FAPROTAX and IJSEM phenotypic database information in the MACADAM database for bacterial and archaea organisms. The fifth key is the number of pathways in a PGDB (numberOfpathway). Bacterial metadatabase that provides strain-linked information about bacterial and archaeal biodiversity, including taxonomy information NCBI Taxonomy A taxonomic database operated by NCBI and concentrating on all taxa for which DNA sequences are available (those sequences are stored by GenBank , another database operated by NCBI). All common gateway interfaces and database interfacing scripts are written in the Python programming language. addition of new high-quality annotated genomes). Here you will find authoritative taxonomic information on plants, animals, fungi, and microbes of North America and the world. Disclaimer: The NCBI taxonomy database is not an authoritative MACADAM contains a total of 7921 metabolites, 592 enzymatic reactions, 2134 EC numbers and 7440 enzymes. The MACADAM database contains 13 509 PGDBs (13 195 bacterial and 314 archaeal), 1260 unique metabolic pathways, completed with 82 functional annotations from FAPROTAX and 16 from the IJSEM phenotypic database. It provides the possibility to explore functional information completed with metabolites, enzymes, enzymatic reactions and EC numbers. (2000) 50:1095-1102. I would appreciate it if you could tell how to make tazonomy for the custom database. At the top, formulas for the computation of the PS and PFS. Reimer, Berlin. The first one is the taxonomy key that is the numeric lineage. MACADAM automatically downloads the new index summary from RefSeq. Syst. Fourth, MACADAM is open access, freely downloadable and the possibilities of consultation are unlimited. Thus, this feature provides functional information about organisms with no functional information based on related taxonomic species. If the median value of the PFS is equal to 0.7, this means these 4 reactions have >1 associated enzymes, 7 enzymes for 10 reactions in all (Figure 2).