How to link chemical search results to enzyme data?
In this tutorial you will learn how to link the results of chemical searches in other tutorials to enzymes and other data.
Content:
How to find enzymes that convert some diacyl-sn-glycerol (DAG) to some triacyl-sn-glycerol (TAG)?
To retrieve reactions then enzymes that convert some diacyl-sn-glycerol (DAG) to some triacyl-sn-glycerol (TAG) click the Advanced search link to access this functionality:
- Click All button, select Reaction participants then ChEBI small molecule field. Enter 'diacyl' and select "a 1,2-diacyl-sn-glycerol [CHEBI:17815]" in the autocompletion list.
- Then redo the same operations for the second molecule, i.e. click All button, select Reaction participants then ChEBI small molecule field. Enter 'triacyl' and select "a triacyl-sn-glycerol [CHEBI:64615]" in the autocompletion list.
Then click Search button to get the result. Your advanced query is translated as
query:
chebi:"a 1,2-diacyl-sn-glycerol [17815]" chebi:"a triacyl-sn-glycerol [64615]"
Note that, by default, the AND operator is used.
This search returns a table with the Rhea reactions that match this constraint (17 reactions in Rhea release 115).
To retrieve the enzymes catalyzing these reactions, you can either click the hyperlink provided in the Enzyme column of the table, or you can select the rows (reactions) of interest in the result table and click the Find enzyme button.
In both cases, you will be redirected to a result page of the UniProt web site. Now, a row is a protein. It offers the possibility for new explorations, e.g. similarly, you can customize the UniProt result table to display the columns of interest.
Come back to the Rhea web site where we want to refine our search by excluding hydrolysis reactions (i.e. by excluding water molecules).
The query is now:
chebi:"a 1,2-diacyl-sn-glycerol [17815]" chebi:"a triacyl-sn-glycerol [64615]" NOT chebi:"H2O [15377]"
The result is now a set of 15 reactions (Rhea release 115) with RHEA:33271 and RHEA:41111 excluded.
Let's take a look at RHEA:10868
We can see that it is an abstract reaction, for which several instances are already annotated in Rhea. You can access to the specific forms by browsing the Related reaction section.
