Protein Database Help Document

Search: You can search the protein database using any of the following: SWISSPROT accession number, SPTrEMBL ID, Protein Sequence Identifier (Protein_ID), Genbank's GI number, protein name, gene name, species or cultivar.

Advanced Search: It allows customized search by the protein name, accession number, protein id (PID) from NCBI/Uniprot/DDBJ, SPTrEMBL ID, GenBank ID, cultivar (germplasm) as well as a selection of the species. In the species list only the major cereal crops are listed. If your species of interest is not in that list please select "All Poaceae family". CLICK HERE to visit advanced search.

Use star (*) before/after/both in your query text to extend your searches. e.g. alcohol*, *alcohol, *alcohol*. Don't put star if you want an exact search.

Search results can be sorted by accession number, names/symbol/synonym or organism (species and cultivar) on the results page. The protein accession number provides a link to the protein detail information page.

Rice Protein page

General Information:

• Name(s):  Shows the names of the protein molecule based on its function or phenotype. Often it is same as the gene name.
• Symbol:  Shows the protein symbol.
• Synonym:  Shows all the alternate names (aliases) by which the molecule is called in various databases and in scientific literature.
• E.C. Number(s):  Shows the designated Enzyme Commission (E.C.) number. The EC numbers link to GenomeNet, Japan
• Gene symbol:  Lists all the gene symbols by which the molecule is called, as designated by the Commission on Plant Gene Nonmenclature or by those cited in literature.
• Best hits to TIGR rice gene models: The link generates a BLASTP query by using the respective protein sequence against the peptide sequences deduced from the TIGR rice gene models. The query retuns a set of best hits on the rice gene models mapped on the TIGR's rice genome assembly of the IRGSP sequence. From the BLAST results page you can use the links to browse the appropriate locus on the rice genome or the TIGR-rice gene model. To learn how to use BLAST search, please visit the BLAST help document
• Accession numbers:  Is the Swissprot accession number, same as the "AC" field from SWALL (EMBL) record and "ACCESSION" field of GenBank record of the respective protein entry. Links the protein entry to the other databases namely, GenBank protein database,  and SWISSPROT-TrEMBL.
• Database references: Provides a link to the corresponding entry in the species specific databases such as GrainGenes (oat, barley, wheat, rye) and MaizeGDB (maize).
• Organism:  Represents the taxonomy of the organism from which the protein sequence or the corresponding nucleotide sequence of the gene was derived.
•  Species:  Shows the Genus and species names and provides link to Gramene's Taxonomy ontology for further information.
•  Cultivar:  The name of the variety/stock/germplasm/cultivar (Cv) from which the sequence was derived. The name of the germplasm repositories, like GRIN and IRIS, link to the cultivar/variety entry (name based search) in these databases.
• Comment:  A simplified text from the curator, describing interesting information about the protein or the gene.

• Associations:

This section suggests the functional characteristics of a protein. The information is provided by means of association to the following controlled vocabularies (ontologies). For more details on ontology and to learn about them please visit the ontology home.
•  Term type and term
•  Gene Ontology (GO)
• Molecular function:  List of GO term(s) suggesting the molecular function of the protein molecule (protein entry)
• Biological process:  List of GO term(s) suggesting the biological process where the function of the respective protein entry is required
• Cellular component:  List of GO term(s) suggesting the localization of the protein entry in the cellular component
•  Plant Ontology
• Plant structure (PO):  List of PO term(s) suggesting the plant structure (anatomical part) where the protein or its transcript (mRNA) is expressed.
• Cereal Plant growth stage (GRO):  List of GRO term(s) suggesting the growth stages when the protein or its transcript (mRNA) is expressed.
• Evidence:  The actual evidence used in inferring the association to an ontology term. The evidence could be an Interpro entry, swissprot entry or a Gramene literature citation.
• Evidence code:  Lists the evidence code suggesting the type of experiment used in making the ascertion on associating the ontology term to a given protein.
• Keywords:  List of keywords that are associated with the protein entry.

• Similarity to other proteins:  The terms under this table link to the BLINK from the NCBI, to find out the homologues / orthologues / proteins having similar 3D-structures with the nearest relative in taxonomic term. Second link to the SAS (Sequence Annotated by Structure) database at UCL, UK, helps you in finding proteins with similar 3D-structures.

• Protein Features:

• Pfam:  Describes the protein family to which the respective protein entry belongs. Links Pfam ID to the respective entry in the Pfam database. (The option is available to view the list of protein database entries at Gramene, sharing this Pfam motif).
• PROSITE:  Describes the various PROSITE signatures the respective protein entry carries. Links PROSITE ID to the respective entry in the PROSITE database. (The option is available to view the list of protein database entries at Gramene, sharing this Prosite motif. The "residues from" section suggests the location of PROSITE domain in the protein molecule.
• Physiochemical features:  Links the protein entry to Expasy for analyses of physio-chemical features by the ProtParam tool.
• Protomap:  Links protein entry to the ProtoMap database at Cornell University.
• Feature Type:  The table provides the list of features other than the Pfam and PROSITE. More details on how the predictions were generated for features namely, Transmembrane click here and Signal Peptide click here. The table shows Feature type, Residues (From-To) suggesting its location on the protein molecule, the Evidence related to feature type and the Evidence code. For details on evidence and evidence code please follow the help on association section.