Gramene Proteins Help Page

Proteins search/browse options

From the Protein home page, enter a keyword into the "Quick Search" Box, and click on the search icon. Search by keyword - protein name / gene name / species / cultivar/ SWISSPROT accession number / SPTrEMBL ID / Protein Sequence Identifier (Protein_ID) / Genbank GI number. Use "*" as a wildcard. Don't use the wildcard if you want an exact search. For example, searching "*dwarf-1*" will give results for dwarf and semidwarf, with numbers begining with "1", such as "1" or "19"

Enter a keyword in the search box. Use "*" for a wildcard, as described above for "Quick Search".

Select the field to search for this term. Options include:

Accession
Protein_ID(PID)
SPTrEMBL ID
GenBank ID(GI)
Cultivar
All Fields

Select the species from a list of available species to search. 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 on the search icon

The Protein Quick Search and Advanced Search will explore only the fields as outlined in Advanced search, above. To search by the Pfam or PROSITE term, use this special search tool.

GO Slim is a condensed set of Gene Ontologies that are specifically selected by curators as being important to Proteins. GO terms include:

Molecular function of the gene product (protein)
Biological process in which the gene product (protein) is involved .
Cellular component where the gene product (protein) is localized.

In the "Associations" section for your term of interest a list of the protein(s) (if any) related with the particular GO term will be displayed, along with the number of proteins. Click on the species of interest.

The next page will list all the proteins for the ontology term. Click on the "Object Acession ID" which links to the Protein page for that protein. (e.g. Q259V3 as an O. sativa protein under "synthesis")

Proteins Search Results

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

Protein Information - The title gives the taxonomy of the organism from which the protein sequence or the corresponding nucleotide sequence of the gene was derived.

Accession: Gramene internal unique accession.
Species: Species which the protein belongs to.
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.
Synonyms: 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 name: Traditional gene names have been used. Some gene names have been modified according to the Gene Nomenclature System.
Organelle
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
Source
GenBank Accessions: Gives the accession field of GenBank record of the respective protein entry. Links the protein entry to the GenBank database.
SwissProt Accession: the Swissprot accession number, same as the "AC" field from SWALL (EMBL) record. Links the protein entry to SwissProt database.
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.
Database References: Provides a link to the corresponding entry in the species specific databases such as GrainGenes (oat, barley, wheat, rye) and MaizeGDB (maize).

Associated Ontologies:

Ontologies
- 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
Term: 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.
Reference: 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: 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. When appropriate the Interpro term offers an evidence for the respective mapping of the GO term to the gene product. These will link to the Interpro database.

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

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.
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).

Database Cross-References: List of all the references used for annotation of this protein. It also gives an option to search in the Gramene Literature database for all the references that may be associated with this entry.

Other Resources

Tutorial	More in-depth than the help pages, use the tutorial for an exaple of using the database, see how it integrates other datasets, and get tips to increase your data search efficiency.
FAQ	Frequently Asked Questions - see what questions users have asked, and get the developers answers.
Evidence codes
Gene ontology (GO) associations	Associations are based on Gramene curation.
Cellular localization predictions	Predotar and TargetP were used to predict localization to plastid, mitochondria and secretory vesiclular localization. The method used is described in Gramene reference 7047. TMHMM (v. 2.0) was used to predict Transmembrane localization. The method used is described in Gramene reference 7047
Release Notes	For more information about the most recent release.

Feedback

Please send comments or suggestions by either using the "Feedback" link at the top of the Gramene pages or by going to the following URL: /db/feedback/send_feedback?refer_from=/protein/index.html

If you find any inconsistencies or mistakes, please communicate them to us by clicking on the "feedback" link. Your suggestions and feedback are highly appreciated by the Gramene staff.