General
This session contains the general information about the locus. "Synonyms" have all the names and synonyms of the locus across different databases. "Description" includes annotation of the locus as well as family annotation if applicable.
Family and Alignment
The PlantsP database includes two types of classifications: kinase classification and phosphatase classification (click on the links for more details). The PlantsUBQ family classification is based on ubiquitin-associtated domain features detected in the protein sequence.The multiple alignment is generated using clustalw and is for the lowest level of sub-family if the protein belongs to more than one level of families. To view the alignment, you can pick MSF or HTML format, or define your own HTML options (display format, sequence selection and consensus option, or display colors), or view it in Jalview.
Protein
Feature scan using known feature scan tools and databases such as pfam, prosite, TMprediction and pfscan. cutoff ratio may vary according to the needs, by default, it's set to 0.001.
Each of color bars in the feature diagram represent the corresponding sequence with scanned features. For sequence with features overlapping, only one color is used for the overlapping area.
To view detailed description of feature scanning methods and parameters click on the color bars in the feature diagram.
User can check the boxes before the targert features and redraw the diagram
Click on fasta button will generate a fasta format sequence
Click on blast button, user can blast search this sequence against different database currently available
Gene Expression Data
Microarray data are from two sources: the AMPL and the genevestigator websites. Click on the diagrams for more details about the data.
Source Name URL Source Description Latest Update Date Genevestigator https://www.genevestigator.ethz.ch Genevestigator is an Arabidopsis gene expression database and analysis toolbox. Arabidopsis locus identifiers and annotations: TIGR version 5.0, January 2004 AMPL (Arabidopsis Membrane Protein Library) http://www.cbs.umn.edu/arabidopsis AMPL is a collection of polytopic membrane protein sequences from Arabidopsis thaliana. Protein sequence dataset: TIGR version 5.0
Protein History and Links to Sources
All the superceded entries in the database are shown here. Data from different sources such as TIGR, Genebank, TAIR are merged into one leading record which is picked using locus name or synonym match, and blastn/blastp search. User can click on the links provided to access the data source for information check.
External Resources
Links to other databases of the particular locus.
Community
Click on the link to start a discussion about the protein. Any user with a login account can add annotation to the protein, but the modified annotation won't be displayed immediately on the web page. The original annotators or domain experts will vote for the proposed change. after approval, the change will be reflected on the web page, and the original annotator(s) and users who has the entry in their favorites will get email notification about the change.
Chronology
Changes made to the database and modification date.
Simple Motif Search
The difference between a Unix-type regular expression and a Prosite Pattern can be demonstrated using a made-up motif:Regular expression: CG.{4,6}G.{3}[NG]Q{GC}
Prosite pattern: C-G-x(4,6)-G-x(3)-[NG]-Q-{GC}.The capital letter defines a particular type of amino-acid residue in both expressions. Prosite pattern uses the dash characters '-' to make it slightly easier to read.
The notation .{4,6} in a regular expression means that at least 4 and at most 6 residues of any type may occur at this position, which corresponds to the notation x(4,6) in a Prosite pattern .
The notation [NG] means the same thing in regular expression and prosite pattern. One and only one residue must be at this position, and any of the residues within the brackets may be chosen.
The notation … or .{3,3} or .{3}in a regular expression corresponds to the notation x(3) or x(3,3) in a Prosite pattern. This means that exactly three residues of any type may occur at this position.
In both regular expression and Prosite pattern, the notation {GC} means that all residues except G and Gly (G) and Pro (P) are allowed in this position.
