※ Related resources & tools
Public databases containing prokaryotic phosphorylation sites
1. dbPTM: An integrated resource for protein post-translational modifications (Huang, et al., 2019).
2. UniProt: A worldwide hub of protein knowledge (UniProt Consortium, 2019).
3. SysPTM: A systematic resource for proteomic research on post-translational modifications (Li, et al., 2014).
4. PHOSIDA: A phosphorylation site database, integrates thousands of high-confidence in vivo phosphosites identified by mass spectrometry-based proteomics in various species (Gnad, et al., 2011).
5. Phosphorylation Site Database: A guide to the serine-, threonine-, and/or tyrosine-phosphorylated proteins in prokaryotic organisms (Wurgler-Murphy, et al., 2004).
Taxonomy annotation
1. BacDive: A comprehensive resource for structured data on the taxonomy, morphology, physiology, cultivation, isolation and molecular data of prokaryotes (Reimer, et al., 2019).
2. LPSN: List of prokaryotic names with standing in nomenclature (Parte, et al., 2018).
3. MicrobeWiki: A free wiki resource on microbes and microbiology, authored by students at many colleges and universities.
4. NCBI Taxonomy: A standard nomenclature and classification repository for the International Nucleotide Sequence Database Collaboration (INSDC), comprising the GenBank, ENA (EMBL) and DDBJ databases (Federhen, et al., 2012).
5. PATRIC: the all-bacterial bioinformatics database and analysis resource center (Wattam, et al., 2017).
6. proGenomes: A resource for consistent functional and taxonomic annotations of prokaryotic genomes (Mende, et al., 2017).
7. fusionDB: A databse assessing microbial diversity and environmental preferences via functional similarity networks (Zhu, et al., 2018).
Genome annotation
1. Mycobrowser: A comprehensive genomic and proteomic data repository for pathogenic mycobacteria (Kapopoulou, et al., 2011).
2. Ensembl Bacteria: A browser for bacterial and archaeal genomes (Kersey, et al., 2018).
3. MicroScope: An expanding and evolving integrated resource for community expertise of microbial genomes (Vallenet, et al., 2017).
4. GOLD: A World Wide Web resource for comprehensive access to information regarding genome and metagenome sequencing projects, and their associated metadata (Mukherjee, et al., 2018).
5. CyanoBase: Providing cyanobacterial genome annotations as references for cyanobacterial research (Fujisawa, et al., 2017).
6. Islander: A database of precisely mapped genomic islands in tRNA and tmRNA genes (Hudson, et al., 2015).
7. PseudoCAP: The Pseudomonas Genome Database, a database for high-quality Pseudomonas aeruginosa PAO1 genome annotation and whole-genome comparative analyses(Winsor, et al., 2016).
8. PAIDB v2.0: A database dedicated to providing comprehensive information on all reported Pathogenicity islands (PAIs) and candidate PAIs in prokaryotic genomes (Yoon, et al., 2015).
9. SILVA: A comprehensive on-line resource for quality checked and aligned ribosomal RNA sequence data (Glöckner, et al., 2017).
10. MicrobesOnline: A comparative genome browser for phylogenomic analysis of microbial communities (Chivian, et al., 2013).
Function annotation
1. ECMDB: Escherichia coli Metabolome Database, a comprehensive database containing detailed information about the genome and metabolome of E. coli (K-12) (Sajed, et al., 2016).
2. AtlasT4SS: A database for analysis of prokaryotic type IV secretion system (Souza, et al., 2012).
3. TADB 2.0: A database of bacterial type II toxin-antitoxin loci (Xie, et al., 2018).
4. ChEMBL: Database of bioactive molecules with drug-like properties (Gaulton, et al., 2017).
5. SwissLipids: A knowledge resource for lipids and their biology (Aimo, et al., 2015).
6. tRNADB-CE: A tRNA gene database manually curated by experts (Abe, et al., 2014).
7. P2CS: A comprehensive resource for the analysis of Prokaryotic Two-Component Systems (Ortet, et al., 2015).
8. TransportDB 2.0: A relational database for exploring membrane transporters in sequenced genomes from all domains of life (Elbourne, et al., 2017).
9. SigMol: A repertoire of quorum sensing signaling molecules in prokaryotes (Rajput, et al., 2016).
10. Enzyme: A comprehensive enzyme information system (Placzek, et al., 2017).
11. EffectiveDB: Pre-calculated predictions of bacterial secreted proteins and of intact secretion systems (Eichinger, et al., 2016).
12. REBASE: A database for DNA restriction and modification: enzymes, genes and genomes. (Roberts, et al., 2015).
13. PSORTdb: Expanding the bacteria and archaea protein subcellular localization database to better reflect diversity in cell envelope structures. (Peabody, et al., 2016).
14. Census of bacterial signal transduction proteins: Signal transduction proteins encoded in genomes of 555 bacterial and archaeal species (Galperin, et al., 2010).
15. PeroxiBase: A database for large-scale evolutionary analysis of peroxidases (Fawal, et al., 2013).
16. EchoBASE: a post genomic database that curates experiments providing new information about genes and their products in the model bacterium Escherichia coli (Misra, et al., 2005).
17. Gene Ontology resource : A resource for structured, computable knowledge regarding the functions of genes and gene products (The Gene Ontology Consortium, 2019).
Transcriptional regulation
1. PRODORIC2: One of the largest collections of DNA binding sites for prokaryotic transcription factors (Eckweiler, et al., 2018).
2. CollecTF: A database of experimentally validated transcription factor-binding sites in Bacteria (Kiliç, et al., 2016).
3. DBTBS: A database of transcriptional regulation in Bacillus subtilis containing upstream intergenic conservation information (Sierro, et al., 2008).
4. RegPrecise 3.0: A database for capturing, visualization and analysis of transcription factor regulons that were reconstructed by the comparative genomic approach in a wide variety of prokaryotic genomes (Novichkov, et al., 2013).
5. CoryneRegNet: The reference database and analysis platform for corynebacterial gene regulatory networks (Pauling, et al., 2012).
6. RegulonDB: Escherichia coli K-12 Transcriptional Regulatory Network (Gama-Castro, et al., 2016).
7. P2TF: A comprehensive resource for analysis of prokaryotic transcription factors (Ortet, et al., 2012).
8. FootprintDB: A database of transcription factors with annotated cis elements and binding interfaces (Sebastian, et al., 2014).
Sequence and structure information
1. Compute pI/Mw: A tool which allows the computation of the theoretical pI (isoelectric point) and Mw (molecular weight) for a list of entered sequences (Wilkins, et al., 1999).
2. MMDB: 3D structures and macromolecular interactions (Madej, et al., 2012).
3. DisProt: A database of protein disorder (Vucetic, et al., 2005).
4. RCSB PDB: A database of biological macromolecular structures (Burley, et al., 2019).
5. IUPred2A: A web interface that allows to identify disordered protein regions using IUPred2 and disordered binding regions using ANCHOR2 (Mészáros, et al., 2018).
Family and domain annotation
1. PIRSF: An integrated public resource of protein informatics (Wu, et al., 2004).
2. CATH-Gene3D: A database for protein structure classification (Dawson, et al., 2017).
3. TIGRFAMs: A resource consisting of curated multiple sequence alignments, Hidden Markov Models (HMMs) for protein sequence classification, and associated information designed to support automated annotation of (mostly prokaryotic) proteins (Haft, et al., 2013).
4. TCDB: A reference database for transport protein research, which provides structural, functional, mechanistic, evolutionary and disease/medical information about transporters from organisms of all types (Saier, et al., 2016).
5. PRINTS: A fine-grained protein sequence annotation and analysis resource (Attwood, et al., 2012).
6. SCOP2: Structural classification of proteins (Andreeva, et al., 2014).
7. InterPro: An integrated resource for protein families, domains and functional sites (Mitchell, et al., 2019).
8. HAMAP: A system for high-quality automated and manual annotation of proteins (Pedruzzi, et al., 2015).
9. ESTHER: A database of the α/β-hydrolase fold superfamily of proteins (Lenfant, et al., 2013).
10. PANTHER: A resource for the evolutionary and functional classification of genes from organisms across the tree of life. (Mi, et al., 2019).
11. PROSITE: A database of protein domains, families and functional sites (Sigrist, et al., 2013).
12. Pfam: A large collection of protein families, each represented by multiple sequence alignments and hidden Markov models (HMMs) (El-Gebali, et al., 2019).
13. SMART: A web resource for the identification and annotation of protein domains and the analysis of protein domain architectures (Letunic, et al., 2018).
Interaction
1. MEROPS: An integrated source of information about peptidases, their substrates and inhibitors (Rawlings, et al., 2018).
2. aBiofilm: A resource of anti-biofilm agents and their potential implications in targeting antibiotic drug resistance (Rajput, et al., 2018).
3. PHI-Base: A database providing expertly curated molecular and biological information on genes proven to affect the outcome of pathogen-host interactions (Urban, et al., 2017).
4. IntAct: An open-source, open data molecular interaction database populated by data either curated from the literature or from direct data depositions (Orchard, et al., 2014).
5. MVP: A microbe-phage interaction database capturing the full dynamics in the interactions between microbes and phages (Gao, et al., 2018).
6. DrugBank: A comprehensive online database containing information on drugs and drug targets (Wishart, et al., 2018).
7. BioGrid: An open access database dedicated to the curation and archival storage of protein, genetic and chemical interactions for all major model organism species and humans (Oughtred, et al., 2019).
8. STRING: Protein-protein association networks with increased coverage, supporting functional discovery in genome-wide experimental datasets (Szklarczyk, et al., 2019).
9. The Complex Portal: A manually curated, encyclopaedic resource of macromolecular complexes from a number of key model organisms (Meldal, et al., 2019).
10. RAID v2.0: RNA-associated interactions across organisms (Yi, et al., 2017).
11. STITCH: Protein-chemical interaction networks with tissue and affinity data (Szklarczyk, et al., 2016).
12. Mentha : A resource for browsing integrated protein-interaction networks (Calderone, et al., 2013).
13. DIP: The Database of Interacting Proteins (Salwinski, et al., 2004).
14. CAMPR3: A database on sequences, structures and signatures of antimicrobial peptides (Waghu, et al., 2016).
Orthologous information
1. COG: A database of Clusters of Orthologous Groups (COGs) of proteins concentrating on prokaryotes (Galperin, et al., 2015).
2. OrtholugeDB: A bacterial and archaeal orthology resource for improved comparative genomic analysis (Whiteside, et al., 2013).
3. ATGC: A resource for micro- and macro-evolutionary studies of prokaryotic genomes and protein family annotation (Kristensen, et al., 2017).
4. EggNOG: A hierarchical, functionally and phylogenetically annotated orthology resource (Huerta-Cepas, et al., 2019).
5. OrthoDB: Providing evolutionary and functional annotations of orthologs (Kriventseva, et al., 2019).
6. OMA: A method and database for the inference of orthologs among complete genomes (Altenhoff, et al., 2018).
7. KEGG ORTHOLOGY (KO): A database of molecular functions represented in terms of functional orthologs (Kanehisa, et al., 2016).
8. InParanoid: A database of ortholog groups with inparalogs (Sonnhammer, et al., 2015).
9. PhylomeDB: A public database for complete catalogs of gene phylogenies (phylomes) (Huerta-Cepas, et al., 2014).
10. HOGENOM: A database of homologous gene families for comparative genomics (Penel, et al., 2009).
Biological pathway
1. BioCyc: A collection of microbial genomes and metabolic pathways (Karp, et al., 2017).
2. WikiPathways: A multifaceted pathway database bridging metabolomics to other omics research (Slenter, et al., 2018).
3. KEGG PATHWAY: A collection of manually drawn pathway maps representing our knowledge on the molecular interaction, reaction and relation networks (Kanehisa, et al., 2016).
4. Reactome: An open-source, open access, manually curated and peer-reviewed pathway database (Jupe, et al., 2018).