In GPS-Lipid 1.0, we tried to make it powerful and convenient to be used. The online service and local packages were provided. This USAGE is prepared for the online service. For usage of local packages, please download the Manual.

Web server

1.Input. In the web server page of GPS-Lipid, users can input one or multiple protein sequences with FASTA format in the text-box or upload a FASTA format file via the file selection dialog box. In order to guarantee a safe run of our web server, a maximal file size of 2M is allowed to be uploaded in each case.

2.Operation. In the bottom of the web server, three operation panels including the PTM panel, the threshold panel and the console panel are provided. The PTM Type panel lists four supported lipid modification types. By selecting one or more modification types, users may conveniently predict any combinations of lipid modifications. For a better prediction performance, three thresholds of high, medium and low stringency were chosen for GPS-Lipid and provided in the threshold panel. In order to balance the prediction performance, the medium stringency was selected as the default threshold. Beside the threshold panel, a console panel was developed. In this panel, we provide several examples to try out the web server.

3.Output. All of the prediction results are presented in a tabular form containing the information of FASTA title, modified position, modified peptide, predicted score, prediction cutoff and modified type. In the position column, the precise lipidation sites are shown. Also, the predicted peptide for lipidation is displayed in the peptide column with the modified site shown in red. The cluster score and its corresponding cutoff are presented in the score and cutoff column, respectively. In the last column, the category of the lipid modification is indicated.

Database

1. Search. You can input one or multiple keywords (separated by space character) to search the GPS-Lipid database. The search fields including LipidDB ID, UniProt Accession, Protein Name, Protein Alias, Gene Name, Gene Alias, Species, and Function.

EXAMPLE: Please click on the "Example" button to search "membrane protein" in Function field. By clicking on the "Submit" button, the related proteins will be shown.

2. Advance Options. Three advance options are provided, including advance search, browse and BLAST search.

(1) Advance search allows you to input up to three terms to find the information more specifically. The querying fields can be empty if less terms are needed. The three terms could be connected by the following operators:

exclude: If selected, the term following this operator must be not contained in the specified field(s)
and: the term following this operator has to be included in the specified field(s)
or: either the preceding or the following term to this operator should occur in the specified field(s)

EXAMPLE: You can click on the "Example" button to load an instance, which could search the cytoskeleton protein in human. The human CKAP4 (LipidDB-9606-00001), which is palmitoylated at C100, will be shown by clicking on the "Submit" button.

(2) Browse You can browse the LipidDB 1.0 database by species and modification types. With the default setting, you can directly click on the "Submit" button to browse all the proteins that are modified by lipid groups in the database.

(3) BLAST search could be used to find the specific protein and/or related homologues by sequence alignment. This search-option will help you to find the querying protein accurately and fast. Only one protein sequence in FASTA format is allowed per time. The E-value threshold could be user-defined, while the default is 0.01.

EXAMPLE: You can click on the "Example" button to load the protein sequence of human HLA class I histocompatibility antigen. By clicking on the "Submit" button, you can find the related homologues in other species.

※ Frequently Asked Questions