1). Protein kinase HMM Profiles. 2). Protein phosphatase HMM Profiles.
In EKPD 1.1, we try to make it more powerful and convenient to be used. This USAGE is prepared for the online service. The EKPD 1.1 provides the browse, search and advance options.
1. Browse. Two simple ways have been provided for users to browse protein phosphatases in database. Users can browse by species or by family classifications. Species browse allows user to choose interested animals, fungi and plants. Family browse allows user to select interested family.
EXAMPLE: Please first click on the species phylogenetic trees or family classification picture and enter specific browse webpage. Then by selecting species or family, the related protein phosphatases will be presented.
2. Search. Four search options are provided, including simple search, advance search, protein classification and BLAST search.
(1) Simple search. You can input one keyword to search the EKPD 1.1. The search fields include EKPD ID, Ensembl Gene ID, Ensembl Protein ID, Ensembl Transcript ID, UniProt Accession, Protein Name/Alias and Gene Name/Alias.
EXAMPLE: You can click on the "Example" button to load an instance. All species containing Akt1 kinase will be shown by clicking on the "Submit" button.
(2) 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)
EXAMPLE: You can click on the "Example" button to load an instance; the human protein kinase ePK/AGC/AKt/Akt1 will be shown by clicking on the "Submit" button.
(3) Protein Kinase & Protein Phosphatase Detection. This section can provide protein kinase and protein phosphatase classification information of an unknown sequence submitted by user, including group, family, score, e-value, domain length and alignment information. If sequence can't be classified into any family, the program will tell you "No hits found". The details of classification method are available in paper.
EXAMPLE: You can click on the "Example" button to load an instance, which could make a classification on given sequence. The result will be presented following by clicking on submit button.
(4) BLAST search. This option is 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 species information could be specified. The default parameters of E-value and species are 0.01 and H. Sapiens, respectively.
EXAMPLE: You can click on the "Example" button to load the protein sequence of human Dual specificity protein phosphatase 7 (DUSP7). By clicking on the "Submit" button, you can find the related homologues in H. Sapiens.
Frequently Asked Questions:
1. Q: Is Protein Kinase & Protein Phosphatase Detection program available for prokaryotic proteins?
A: The data in EKPD 1.1 is predicted and classified with HMM profiles derived from protein kinase and protein phosphatase catalytic domain of eukaryotic proteins. As the HMM profiles represent the feature of eukaryotic protein kinase and protein phosphatase, and divergences exist in the evaluation of eukaryotes and prokaryotes, it is not recommended to make a classification for prokaryotic protein.
2. Q: Is it available to carry on protein kinases or protein phosphatases classification for multiple proteins at the same time?
A: In order to make a rapid classification, we recommend only one input protein. Actually, later, we will offer a local program to accomplish the batch search work.
A: The protein is annotated as reviewed or unreviewed according to its quality of annotation information. For example, if a protein is annotated as "Reviewed" in UniProtKB, we will also mark it as "Reviewed". If a protein cannot be mapped to UniProtKB or it is "Unreiewed" in UniProtKB, we will annotate it as "Unreiewed".
4. Q: I have a few questions which are not listed above, how can I contact the authors of EKPD?