BioCatNet Web Interface

Search

Sequences

Structures

Functions

Taxonomy


Search

Click the magnifying glass on the upper right to open the search panel, where you can choose what exactly you want to find.

Quickjump

Jump quickly to specify sequence, protein or any other entity by providing its ID. Different IDs are used throughout the BioCatNet to identify different types of entries. [T#xxx] will identify a taxonomy entry, for example. Simply hit ENTER after typing in the ID to jump.
  • [T#xxxxx] Taxon
  • [S#xxxxx] Sequence
  • [P#xxxxx] Protein
  • [HF#cxxx] Homologous Family
  • [HFG#xxx] Homologous Family Group
  • [SF#xxxx] Superfamily
  • [SFG#xxx] Superfamily Group

Fams/Prot/Seqs

This tab opens a form where you can find superfamilies, homologous families, proteins or sequences with user-defined properties like names, number of subordinate elements or number of included structures. Choose different compares to find items where the chosen property matches (=), does not match (!=), is similar (~) or is smaller/larger (</>) to the value you provide.

Taxonomy

allows you to search for taxons by organism name. Activating "only those with seqs." will bring up only those organisms, which were found to contain proteins included in the database. Otherwise, all matching organisms will be listed.

Sequences

contains the sequence browser. Sequence information on BioCatNet is classified in a hierarchical order containg six tabular groups ranging from sequences to superfamily groups. Several sequences may belong to a single protein. Proteins are grouped into families of homologous proteins (HFam) by sharing similar sequence patterns. Families of homologous proteins are grouped in superfamilies (SFam). According to similarities in sequence and function families of homologous proteins and superfamilies are summarized in extra groups (HFam groups and SFam groups).

The six hierarchical groups represent the six columns below the pie charts. By clicking on the name of a certain superfamily the user is guided to several families of homologous proteins and thereby gets access to various single sequence entries. Clicking on the name of a protein redirects to a page where different parts of information are collected including the annotated sequence, the biological source and (if available) information regarding structure and/ or function of the desired protein entry. Sequence information is parsed via NCBI accession numbers.


Structures

Protein structure is parsed from PDB entries into the BioCatNet system. Under the Structures bar PDB entries are available grouped by superfamilies, families of homologous proteins, proteins, sequences and source organisms.


Functions

One of BioCatNet's main features is the availability of data regarding biochemical functions such as experimental conditions or enzyme kinetics. Experimental scientists can submit their data after registration. For submission certain parameters are required in a virtual lab journal.

To enable consistent comparison of biochemical data certain information for the biocatalyst and the experimental conditions is mandatory. This includes the scale of the experiment (initial volume), a description of the reaction (including educts, products and their stoichiometry), detailed information on the biocatalyst(s), educts and products as well as description of buffer and solvents.

Optional information may include description of additive compounds, kinetics and experimental conditions (e.g. pH, temperature, pressure).


Taxonomy

The TaxonomyBrowser will allow you to walk through the taxonomy tree, and display linked information like the lineage, synonyms, sibling and child nodes and sequences from our database that are linked to this taxon. The taxonomy ID that prepends every taxon entry is the same that is used by the NCBI. Clicking on the question mark that follows every taxonomy entry will present you a list of synonyms. The chain icon denotes taxonomy entries that are linked to one or more sequences in our database. The beaker icon denotes sequence entries that have linked functional information, and the swivel will tag sequences with linked structure information.