input options

select Entries from databse

or upload UniProt IDs as csv file

output options

select the kinds of motifs to include


motifs in the selected proteins:


motifs in the selected proteins (max. 100 proteins):

input options

paste amino acid sequences

or upload sequences as plain text (.txt)

output options

select the kinds of motifs to include


motifs in the selected proteins:


motifs in the selected proteins (max. 100 proteins):

KFERQ finder app programmed in R using Shiny


Version 0.85 2018 08 04

CMA-targeting (KFERQ-like) targeting motifs can be searched in all human, mouse or rat proteins in UniProt
KFERQ-like motifs belong to different classes based on their amino acid composition. For example, motifs with a serine, threonine or tyrosine can be grouped together as phosphorylation-activated motifs and lysine instead of the terminal glutamine belong to the group of acetylation-activated motifs.
There are more advanced groups of motifs combining different modification that are disabled by default because less experimental evidence is available for their function in CMA.


1. motifs from database

input options

UniProt identifiers can be selected from a drop down list for the three available organisms (human, mouse, rat). As an alternative, UniProt identifiers from these species can be uploaded as comma-separated (.csv) tables for batch processing. The input file is assumed to contain a column header

output options

Motif classes can be selected to be searched for in the input proteins. By default the most well characterized classes are selected. If a protein contains none of the selected classes but of other classes this will be mentioned in the results table.
KFERQ-like motifs may be inactivated through ubiquitination. Possible ubiquitination sites in KFERQ-like motifs can be shown in the output table.

results

The motifs identified and some information such as the protein names are displayed in the output. The results table can be downloaded as comma-separated (.csv) file. In addition to the table output format motifs can also be displayed as colored text within the amino acid sequence. This output format is limited to 100 sequences. Longer input should be split accordingly
This output format can be downloaded as a html file.


2. motifs from sequence

input options

To identify motifs in amino acid sequences not available in the UniProt data sets FASTA-style sequences can be analyzed directly.
Lines starting with a ">" are interpretated as headers containinf a sequence description. Multiple sequences should be separated by a line break. Sequenes can be copy-pasted directly into the text input field or uploaded as plain text (.txt) files.

output options

The same output options are used as when identifying motifs from data base entries.

results

Outputs are the same as for motifs from data base