Tutorial
Search a protein in Revenant
Revenant entries can be searched using the text boxes on the top right corner of the page or in the middle of the home page. The user can search by keywords referring to protein name, structure or the Revenant ID, as it is shown in the next figure:
Browse the database
It is also possible to explore all proteins deposited in Revenant using our Browse utility. You can choose between two visualization forms:
List of all proteins: which shows all the Revenant entries according with their ID and displaying also a minimal information about each entry.
Protein timeline: which shows all the Revenant entries ordered by their estimated chronological time and the relevant biological events in the history of life on Earth.
Entry page
Once the entry has been selected, using any of the two mentioned ways, it is possible to access to each entry page. Next figure shows the entry with Revenant ID = RV35
In the first part of the page, the Revenant ID followed by the protein name are shown. Below that, a brief description of the ancestral resurrection is mentioned along with the estimated geological time.
In the section “Ancestral Sequence Reconstruction” we offer information about the tools and models used for the sequence reconstruction, including the obtained sequence with its corresponding name.
The sequence section includes a search utility for sequence patterns which are then highlighted in the corresponding sequence.
In the bottom part of each entry we can find structural information. By clicking in each of the tabs with the different structures for a specific Revenant entry, it is shown further information of the structure such as crystallization method, resolution, GO terms, sequence corresponding to the SEQRES field from PDB database, presence and type of the co-crystallized ligands.
Below the Structures Sections some of the Revenant proteins have annotations about biochemical and/or physicochemical parameters about the resurrected protein. These parameters appear in the Protein Physicochemical parameters section. Some of these para like kcat and Km are substrate specific so they are also listed too.
At the bottom of the page in each Revenant entry is shown the corresponding primary citation of the resurrected protein.
