>sp|P0AE03|TRMJ_SHIFL tRNA (cytidine/uridine-2'-O-)-methyltransferase TrmJ OS=Shigella flexneri GN=trmJ PE=3 SV=1
>sp|Q0T2G7|TRUA_SHIF8 tRNA pseudouridine synthase A OS=Shigella flexneri serotype 5b (strain 8401) GN=truA PE=3 SV=1
>tRNA Arg ICG Escherichia coli
>tRNA Arg UCU Escherichia coli
>tRNA Arg CCU Escherichia coli
The exemplary output for the demo input can be found at
Description of results:
- If any modifications were predicted for a particular position in the query tRNA sequence you can click on this possition on the results page to see the list of predicted modifications.
- The list of possible modifications in each position of the analyzed tRNA sequences comprises the maximal set of possible structures (for hypermodifications all intermediates are included in the list).
- Detailed information about the prediction results includes:
- the name of the query protein which was predicted to work on this position
- the enzyme from the MODOMICS database which was predicted to be homologous to the query protein
- the reaction catalyzed by the enzyme
- the score of the HHsearch program used to predict homology between the proteins: probability and E-value of the hit
- information whether the particular query protein was predicted to be homologous to enzymes with different activities (ambiguity of the prediction)
Additional phylogeny filtering:
Automatic tRNA alignment:
- Knock-out analysis can be performed based on results of previous predictions. If you want to check how the predicted modifications change after knock-out of one or more proteins
go to: knock-out job submission page. There you can provide the id of your previous prediction job together with a list of names of proteins
which should be treated as knocked-out. The names of proteins must be identical to the ones used in your previous prediction. The knock-out analysis will be performed within several minutes.