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.
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.
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