1 - 50 of 72 results


An integrated source of information about peptidases, their substrates and inhibitors, which are of great relevance to biology, medicine and biotechnology. The hierarchical classification of the database is as follows: homologous sets of sequences are grouped into a protein species; protein species are grouped into a family; families are grouped into clans. There is a type example for each protein species (known as a 'holotype'), family and clan, and each protein species, family and clan has its own unique identifier. Pages to show the involvement of peptidases and peptidase inhibitors in biological pathways have been created. Each page shows the peptidases and peptidase inhibitors involved in the pathway, along with the known substrate cleavages and peptidase-inhibitor interactions, and a link to the KEGG database of biological pathways. Links have also been established with the IUPHAR Guide to Pharmacology.

BRENDA / BRaunschweig ENzyme DAtabase

Contains manually annotated literature-based data on a wide range of aspects of enzyme function, their metabolic role, involvement in disease processes, genomic and protein sequences, and enzyme structures. The characterized enzymes cover all taxonomic groups ranging from eukaryotes, archaea, bacteria to viruses. The enzyme information is categorized according to the Enzyme Commission (EC) nomenclature, the enzyme classification system of the IUBMB (International Union of Biochemistry and Molecular Biology).

CAZy / Carbohydrate-Active Enzymes database

Describes the families of structurally-related catalytic and carbohydrate-binding modules of enzymes that degrade, modify or create glycosidic bonds. CAZY is a knowledge-based resource that aims to link the sequence, the specificity and the 3D structural features of CAZymes, the Carbohydrate-Active enZymes. The CAZomes listed in the CAZy website correspond to protein models of finished genomes, i.e. with proteins released in the daily releases of GenBank.

iUUCD / integrated annotations for Ubiquitin and Ubiquitin-like Conjugation Database

Provides a systematic resource for ubiquitin and ubiquitin-like conjugations. UUCD is a comprehensive database that contains almost 57 000 enzymes for ubiquitin and ubiquitin-like conjugation across 70 eukaryotic species. The classification and domain profile information were provided for each regulator, whereas a number of basic annotations such as Ensembl/UniProt accession numbers, gene/protein names, protein/nucleotide sequences, domain/motifs, functional descriptions and GO terms were taken from Ensembl and UniProt databases.

CSA / Catalytic Site Atlas

A database documenting enzyme active sites and catalytic residues in enzymes of 3D structure. We defined a classification of catalytic residues which includes only those residues thought to be directly involved in some aspect of the reaction catalysed by an enzyme. CSA 2.0 provides a new modern interface to a much-extended manually curated dataset of residues involved in enzyme catalytic sites and the functional role they play in the reaction. A new method for reliably extrapolating the annotations and identification of catalytic residues to homologous structures has been implemented. In addition the curated entries can be used to build 3D templates of the catalytic sites, which in turn can be used to search new structures for catalytic site identification using a revised CSS service. Furthermore a new ontology has been developed to permit the transfer of annotations relating to enzyme catalysis between resources.

ENZYME / Enzyme nomenclature database

Contains information related to the nomenclature of enzymes. ENZYME is structured so, it is usable by human readers as well as by computer programs. It describes each type of characterized enzyme for which an Enzyme Commission number has been provided. The database contains 5946 enzymes and can be accessible through the web portal or downloaded. It is searchable thank to different parameter as enzyme class, chemical compound, alternative name, cofactor and other.

Degradome database

Contains the results of the manual annotation of every protease gene in the genomes of human, chimpanzee, mouse, and rat, along with relationships between protease alterations and hereditary diseases. The annotations about each individual protease can be retrieved by browsing catalytic classes and families or by searching specific terms. This Degradome database also provides detailed information about genetic diseases of proteolysis, a growing field of great importance for multiple users. Finally, the user can find additional information about protease structures, protease inhibitors, ancillary domains of proteases and differences between mammalian degradomes.


A resource that brings together protein sequence, structure and functional information, including overall chemical reaction and mechanistic data, for structurally defined domain superfamilies. FunTree uses the CATH classification to annotate and analyse super families of enzymes. In particular the relationships between known 3 dimensional structures, associated sequences and the enzyme chemistry is highlighted. This can be used to place structures and sequences in context of their evolution and the range and similarities/differences in the reaction chemistry (both bond order changes and small molecule substructure). In addition it can be used to infer the possible range of reactions of enzyme structures and sequences that do not have a known function as well as indicating other reactions or substrates available to an enzyme that as yet may not have been observed (enzyme promiscuity).

BYKdb / The Bacterial protein tYrosine-Kinase database

Provides information about Bacterial tyrosine kinase (BYK) sequences with standardized annotations, updated on a monthly basis. BYKdb is divided in two parts: the static part includes general information about BY-kinases with links to other external resources (‘BYK’ link) and pre-computed datasets. The dynamic part contains generic or specialized tools which allows to make annotation of one or several sequences, access to information such as domains and sites are on the BY-kinase sequence.


Provides a human kinase interactome resource. PhosphoPOINT is a comprehensive human kinase interactome and phospho-protein database. This database integrates phospho-proteins, serine/ threonine/tyrosine kinases, and their corresponding protein–protein interaction (PPI) datasets, their potential substrates and their interacting (phospho)-proteins. It also provides annotation that helps to bridge between kinase and its potential substrates using available PPI and coding single nucleotide polymorphism (cSNP) datasets.


A manually curated sequence and amino acid motif database gathering all the different phycobilin lyases and related protein sequences available in public databases. CyanoLyase provides an extensive collection of phycobilin lyases and related proteins, classified in clans, subclans, families and subfamilies. The website also gives access to bioinformatic tools to ease the annotation of these sequences in forthcoming genomes of phycobiliprotein-containing organisms. As such, the website will be updated regularly as new data become available and will therefore be a long-term resource. Users can monitor directly from the web interface the latest changes that have occurred in the database using the corresponding scrolldown menu.


A comprehensive and fully curated database of information about the components of restriction-modification (RM) systems. REBASE contains fully referenced information about recognition and cleavage sites for both restriction enzymes and methyltransferases as well as commercial availability, methylation sensitivity, crystal and sequence data. From the REBASE website users have a variety of resources available that facilitate the analysis of sequence information, including tools for analyzing sequences (REBASE TOOLS), that allow restriction enzyme recognition sites to be found in submitted sequences (NEBCUTTER) and an implementation of BLAST to allow searching against all sequences in REBASE.

dEMBF / Database of Enzymes of Microalgal Biofuel Feedstock

The first curated and integrated web-based relational database on the entire repertoire of enzymes responsible for lipid synthesis in microalgae. dEMBF catalogues the complete list of identified enzymes along with their computed annotation details including length, hydrophobicity, amino acid composition, subcellular location, gene ontology, KEGG pathway, orthologous group, Pfam domain, intron-exon organization, transmembrane topology, and secondary/tertiary structural data. Furthermore, to facilitate functional and evolutionary study of these enzymes, a collection of built-in applications for BLAST search, motif identification, sequence and phylogenetic analysis have been seamlessly integrated into the database. dEMBF is the first database that brings together all enzymes responsible for lipid synthesis from available algal genomes, and provides an integrative platform for enzyme inquiry and analysis.

M-CSA / Mechanism and Catalytic Site Atlas

Provides annotation on the protein, catalytic residues, cofactors, and the reaction mechanisms of hundreds of enzymes. M-CSA is an online resource is complementary to other mechanism databases like the Structure-Function Linkage Database (SFLD), which annotates diverse enzyme superfamilies (groups of enzymes that are evolutionarily related and perform a disparate set of overall chemical transformations utilising conserved chemical components).


Collects information about carbohydrate-active enzyme (CAZymes). dbCAN-seq includes pre-computed sequences and annotations for more than 5,300 bacterial genomes. The database provides, for each Cazyme, an extensive functional annotation page including data such as Conserved Domains Database (CDD) functional domains, sequence homologs in databases CAZy or predictions of signal peptides using SignalP. The repository also contains a metadata page and a tool to identify physically linked CAZyme gene clusters.

IRED / Imine Reductase Engineering Database

Hosts a repository dealing with imine reductases (IRED). IRED is a database, part of the BioCatNet platform, that aims to investigate sequence-structure-function relationships of a specific item. It contains data relative to more than 1400 sequences and 8 structures, classified according 14 superfamilies. Information can be explored by sequences, structures, functions or taxonomy. It can be used for IREDs forecasting by exploiting sequence similarity with known IREDs and b-hydroxyacid dehydrogenases (b-HADs).

TEED / Thiamine diphosphate Dependent Enzymes Engineering Database

Provides access to information about Thiamine diphosphate (ThDP)-dependent enzymes. TEED is a resource of ThDP-dependent enzymes that combines information on the individual protein families, sequence alignments and annotation of the conserved pyrimidine (PYR) and pyrophosphate (PP) domains. The database contains more than 12000 sequence entries which were assigned to 9443 different proteins and 379 structure entries. It can be accessed on the level of sequence, structure, or organism.

The L. monocytogenes 10403S BioCyc database

A resource for researchers studying Listeria and related organisms. The L. monocytogenes 10403S BioCyc database allows users to (i) have a comprehensive view of all reactions and pathways predicted to take place within the cell in the cellular overview, as well as to (ii) upload their own data, such as differential expression data, to visualize the data in the scope of predicted pathways and regulatory networks and to carry on enrichment analyses using several different annotations available within the database.