Reactions Legend

Index:


BioMeta

Returns you to the home page of the BioMeta database.


Molecules

Brings you to the Molecules menu.


Reactions

Brings you to the Reactions menu. Is inactive (and shown in red), because you are already there!


Enzymes

Brings you to the Enzymes menu.


Sources

Brings you to the Sources menu.


Message area

The area were any message is shown (with error messages shown in red and others in blue).


Help

This hyperlink brings you to the clickable map with help texts on all items in the menu (which you are now reading).


Reaction diagram

When a reaction hit is on display, the compounds participating in the reaction are displayed with an arrow separating the reactant(s) from the product(s). Below each compound a hyperlink is available to bring you to the molecular information on that compound. Below the reaction arrow a hyperlink ("Enzyme(s)") is available to bring you to the enzyme(s) catalyzing the reaction (if any). Presently, there is no query option associated with the reaction diagram.

The direction/reversibility information on the reaction is reflected by the reaction arrow (see also the section on reaction direction: the right and left arrows are self-explanatory; for a reversible reaction two arrows are used; and for the remaining cases (unknown direction) a question mark is placed over the (double-pointed) arrow.

Molecular structures in the reaction diagram are displayed using the Java Molecular Editor by Peter Ertl (Novartis).


#

The database entry number. Included for sake of completeness, but not very useful as a query option unless you know entry numbers (which are not intended for identification of entries, unlike the ID strings). Note that only simple numbers can be used here, no ranges or relational operators.


ID

Allows you to search the ID strings of reaction entries. This is a case-insensitive text query option.


Reaction description

This field contains a textual description of the reaction, using the common names of the participating compounds. The arrow depicts the direction/reversibility also shown in the reaction direction field: "-->" if the reaction goes from left to right;" "<--" if the reaction goes from right to left;" "<=>" if the reaction can go in both directions;" or "<?>" if the direction is unknown. The direction/reversibility information is obtained from KEGG's reaction_mapformula.txt file (which itself is derived from the KEGG maps). This is a text query option.


Reaction balance

The balance information on the displayed reaction: "Yes" if the reaction is balanced; "No" if the reaction is unbalanced, followed by a chemical formula representing the difference between the reactants and products; "Unknown" if one or more compounds have a polymeric structure or do not have a structure at all.

The reaction balance information can be searched using the terms "yes", "no", or "unknown" (case-insensitive and only the first character is used for matching).


Reaction direction

The direction/reversibility information on the displayed reaction: "Right" if the reaction goes from left to right; "Left" if the reaction goes from right to left; "Either" if the reaction can go in both directions; or "Unknown" if the direction is unknown. The direction/reversibility information is obtained from KEGG's reaction_mapformula.txt file (which itself is derived from the KEGG maps).

The reaction direction information can be searched using the terms "right", "left", "either", or "unknown" (case-insensitive and only the first character is using for matching).


External links

Hyperlink to the entry from the Reaction section of the KEGG Ligand database. The actual value for this field is the KEGG Reaction accession number (Rnnnnn). This is a case-insensitive text query option.


Search

Submit the query with the query options filled in on the form. All query options are automatically combined in an "and" fashion.


Create

Allows to create a new entry. This option is inactive if you do not have the right to modify the database.


Delete

Allows to delete the current hit. This option is inactive if you do not have the right to modify the database.


Update

Allows to update the current hit. This option is inactive if you do not have the right to modify the database.


Clear

Clears the whole menu and redraws it as an empty input form.


First hit

Brings you to the first hit in the hit set. This option is inactive if the hit set contains just one hit.


Prev hit

Brings you to the previous hit in the hit set. This option is inactive if the hit set contains just one hit.


Next hit

Brings you to the next hit in the hit set. This option is inactive if the hit set contains just one hit.


Last hit

Brings you to the last hit in the hit set. This option is inactive if the hit set contains just one hit.


Goto hit

Brings you to a particular hit in the hit set. This option is active only if you are browsing a hit set with more than three hits. Just type a number in the input field to the right of the "Goto" button, and click on the "Goto" button.


Text query options

Text query options are string searches. They are case-sensitive unless indicated otherwise. Wildcards (using "*") can be used, e.g., "*ucos*phosphate".


Integer number query options

These query options are searches for integer values, allowing comparison and range specifications, e.g., "28", ">=0", "10-19", ">222", and "<=9". Real numbers are not allowed.


Real number query options

These query options are searches for real (floating-point) values, allowing comparison and range specifications, e.g., "3.14159", ">=0.0", "10.51-19.49", ">222.2", and "<=9". Integer numbers are allowed. Note that exponential notation is currently not implemented.