1. Welcome to the Protein Database Tutorial
This tutorial will describe how to navigate the section of Gramene that provides collective information on proteins from grasses (family Poaceae/Gramineae). The protein entries are annotated by associating the following ontology concepts if known:
Gene Ontology (GO)
Molecular function of the gene product.
Biological process in which the gene product is involved.
Cellular component where the gene product is localized.
Plant Ontology
Plant structure where the gene is expressed (PO)
Plant growth stage at which the gene is expressed (GRO)
From the Protein database you can:
Search the protein database using the protein name, gene name, species, cultivar, SWISSPROT accession number, SPTrEMBL ID, Protein Sequence Identifier (Protein_ID) or Genbank GI number.
Determine if a protein is an enzyme.
Map a protein and view neighboring genes and features.
Determine the name of the protein’s gene and view its general information.
Get information on a protein and its features, similarities to other proteins and associations with ontology terms.
Explore protein families (Pfam).
Find the sequence information for a protein.
Identify literature on a protein.
* Only rice (Oryza) protein entries are manually curated.
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2. Tutorial Tips
Note! Although we continually work to make Gramene compatible with all browsers, there are problems with some browser versions. If you're having difficulty viewing Gramene, try using a different browser. Please report any problems with browsers through Gramene Feedback.
Images shown may not be up to date, so results on your searches may be different, or the data may be displayed in a different order.
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3. Click here to open Protein Home Page
Gramene Home Page
Click here to open Protein Home Page
On the Gramene Home Page ( Hover your mouse over “Search” on the navigation menu, and click on “Protein” from the drop-down menu. You can also click on ‘Proteins’ under the quick start section.
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4. Module Home-Page layout
Module home pages provide the following information:
Searching/Browsing – links to different types of searches.
Other Tools – if applicable, links to different tools used in this module.
Help – links to help pages, tutorials, release notes, FAQ and other helpful documentation.
Download – information on where to download the database.
Feedback – How to contact Gramene
Acknowledgements – Other programs that contribute to this data.
Quicklinks and external links – when appropriate these links are provided.
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5. Search Proteins D This is the Protein Home Page
2. Click to limit search by species or object type. (slide 6)
Search Proteins
4. Click to browse by Gene Ontology (slides ) (See Ontology tutorial)
3. Click to Search by Pfam or PROSITE (slides 11-13).
1. Search by entering a term and clicking search icon (slides 7-10.) D
Possible searches. Click some examples to get you started.
You will see the Protein Menu displayed after the grain icon, with the options for Protein Home, Advanced Search, Search by Pfam or PROSITE, Browse by GO Slim, Documents, Tutorial, FAQ and Help.
There are four (4) options for searching for a protein in the Protein Database: 1) Term or Keyword, 2)Advanced Search, 3) Pfam or PROSITE, and 4) Gene Ontology. ". 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.
If your query finds more than 500 matching records, only the first 500 will be displayed. To see all the matching records you will be directed to another link, showing only the Accession Numbers in a table, which will link to the entry in our rice protein database.
This is the Protein Home Page
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6. Advanced Search
Enter a term. 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
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". 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.
Click “search”
Select the field your term is in. Select “All fields” if you are uncertain.
Optionally, select a species to search.
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7. Results for Search by Term or keyword
1. Term Search: Results using “heading date”
Results for Search by Term or keyword
Indicates Search Parameters
To order results by column, click on the hyperlinked column titles.
The results will offer you the Gramene Accession Number, Names/Symbols/Synonyms, Cultivar, and Evidence.
**Note – Gramene databases provide genomic information available for cereals and other grasses. It is up to you, the user, to interpret the data.
Search results can be sorted by accession number, names/symbol/synonym or organism (species and cultivar) on the results page by clicking on the selected header. The protein accession number provides a link to the protein detail information page. .
Click the accession number to view the detail information page for a protein (next slide)
Lists the type of experiments carried out to ascertain the protein’s function. Click to obtain more information.
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8. Protein Detail: General Information
General Protein Info
Protein Detail: General Information
Shows the names of the protein molecule based on its function or phenotype. Often it is same as the gene name.
Species from which the gene was sequenced, links to Gramene's Taxonomy ontology
All the alternate names (aliases) by which the molecule is called in various databases and in scientific literature
Shows the designated Enzyme Commission (E.C.) number. When available, the EC numbers link to GenomeNet, Japan
Click for gene detail (See Genes tutorial)
Click for BLASTP query to find best match(es) to peptide sequences deduced from the TIGR rice gene models.
Cross references to GenBank and SWISSPROT protein entries.
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.
Cultivar (stock) from which the gene was sequenced.
Click for FASTA sequence
Associated Data
A textual description of the protein
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9. Protein Detail: Associations
Protein Associations
Click to view the Reference(s) used to assign the ontology term.
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.
Lists the type of experiments carried out to ascertain the protein’s function. Click on a code for it’s explanation.
Click terms to view Ontology Information (See Ontology Tutorial)
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10. Protein Detail: Similarities
Click these options to link to NCBI’s BLink to display the graphical output of pre-computed BLASTP results against the non-redundant (nr) protein database from NCBI.
Click these options to find if there are any known proteins that share the structural homology with the given protein
Click to learn more about the Protein Family to which the protein belongs (if applicable).
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.
Lists of all the references used for annotation of the selected protein.
Click to view a list of other protein entries that belong to this Protein family or share the Pfam/PROSITE domain.
Click to link to protein entry in other databases.
Click to see Literature Detail Page for that reference (See Literature tutorial).
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11. Search by Pfam or Prosite
From the protein search section, click on the “Search by Pfam or PROSITE” for this search option.
From the Protein Home Page click on “Search by Pfam or PROSITE” to open the search page. This search will list proteins in Gramene that have ID’s in Pfam and PROSITE. Search by either a name or an id.
*Note: Some proteins do not have associations to Pfam and PROSITE features. This will restrict your search.
Search Pfam / PROSITE by either a name or an id as given in examples.
*Note: Some proteins do not have associations to Pfam and PROSITE features. This will restrict your search.
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12. Results Pfam/Prosite search
Results of Pfam or PROSITE Search
Pfam Accession IDs. Click to find proteins in that protein family (see next slide)
The off-site database that shares protein information with the Gramene database
Actual name of the Pfam/PROSITE Class.
For an example, this slide shows a search for “Cytochrome.” The off-site database that shares protein information with the Gramene database is identified in the column labeled “Type.” Clicking on the linked ID – will give you a table of other proteins in that protein family
PROSITE Accession IDs. Click to find proteins that belong to that ID.
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13. List of Proteins belonging to Pfam or PROSITE Entry
Pfam/PROSITE ID
List of Proteins belonging to Pfam or PROSITE Entry
Download the ids/accessions in various formats
Matrix displays summary of all the Pfam/PROSITE domains the given list of proteins share in addition to these (e.g PF00033).
Click to link with the Pfam or PROSITE database for more information.
Protein Name as recorded in Gramene. Click to view the detail information.
Click to view the Swiss-Prot protein entry page.
Click to view the GenBank (NCBI) protein entry page.
The Protein Family Information provides the following information:
The title of the table (Proteins that belong to …) identifies the Protein Family, and links to the Pfam or PROSITE database, where you can get more information on that family.
The Protein Name is the name as recorded in Gramene. Click to view the detail information. (refer to Figures 4-10).
The SPTrembl Accession, and a link to the Swiss-Prot protein entry page.
The GenBank Accession, and a link to the NCBI protein entry page.
Links to Pfam extended information on the Pfam protein (only for Pfam proteins).
A tab-delimited format of Protein IDs that can be downloaded.
A Matrix of the summary of all the Pfam/PROSITE families that the given list of proteins share (in addition to the displayed one).
Click to view the Pfam annotation (column not available for PROSITE).
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14. Browse by GO Slim Search GO Slim
Click to search category in GO
(See Ontology tutorial).
Search GO Slim
From the Protein Home Page click on “Search by GO Slim” to open the search. This search will search the Plant Ontology and Gene Ontology database for associated proteins. (This was discussed above for slide 8) This option is a more direct way to go to the ontologies than the term or keyword search above.
Click on Molecular Function, Biological Process, or Cellular Component to browse that category in Gene Ontology (GO), or click a term listed below the category headings to quickly browse the Ontology database to find a list of proteins associated with these particular keywords. Refer to the Ontology Tutorial for specifics on searching that database.
Note: Many proteins do not have associations to Gene Ontology (GO) terms. This will restrict your search.
Click a term to quickly browse the Ontology database to find a list of proteins associated with these particular keywords
(See Ontology tutorial).
Note: Many proteins do not have associations to Gene Ontology (GO) terms. This will restrict your search.
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15. Results for GO Results for GO Slim
Number of items associated with this term.
The term’s lineage in a molecular function category tree, and its children.
Results for GO
+ Icon informs you that child terms exist. Click the term to expand the tree.
The GO term details include name, synonyms, definition and comments (if any).
The term’s lineage in a molecular function category tree and its children.
Expandable tree icon informs you that child terms exist.
A summary of the total number of Annotations to the given Gene Ontology (GO) term. Click on numbers to find more detail.
Number of proteins associated with this term.
A summary of the total number of Annotations to the given Gene Ontology (GO) term.
Links to Gramene proteins associated with term.
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16. FAQs Search FAQ Feedback: Submit a question to Gramene
Click to expand or collapse a question or answer
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17. Help
Help document provides definitions of terms used, as well as hints for searches.
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18. Email Gramene at gramene@gramene.org
Contact Gramene
Use the feedback button, located at the top of every page, to provide feedback or to ask questions about Gramene. or
Gramene at
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