Gene/Protein/RNA Search Form

organisms/databases currently selected

When multiple databases are selected here, then the specified search criteria will be applied across all selected databases. Note that if many databases are selected, queries can take a substantial amount of time to complete. For this reason, a maximum of 70 databases can be selected. Note that some search criteria may not be available for multi-databases searches.

Enter a gene name, or a database identifier from this database or from an external database to which this database contain links. Partial names will generate a substring search on gene names only (not on database identifiers).
Examples: "trpA", "trp", "b1236"

Enter a protein or RNA name, an EC number, or a database identifier from this database or from an external database to which this database contain links. Partial names will generate a substring search on protein or RNA names only (not on database identifiers).
Examples: "tryptophan synthase", "P0A877", "1.1.2.3"

<= Sequence Length <= nucleotides amino acids

<= Map Position <=

Map position is specified in base pairs from the start of the replicon.

<= Molecular weight (kilodaltons) <=

In this context, monomers refer to polypeptides that are not known to form multimeric complexes, whereas "all polypeptides" includes those that form multimeric complexes as well. Multimers can be either homomultimers or heteromultimers. Proteins also include modified proteins and complexes that contain proteins.

<= Protein copy number <=

Search for all proteins for which the specified small molecule plays one or more of the following roles: Enzyme activator
Enzyme inhibitor
Enzyme cofactor
Enzyme or transporter substrate
Transcription factor ligand

Small molecule:

Enter a compound name and check one or more boxes. Use the autocomplete functionality to select a full compound name, as no substring matching is done on the compound name.
Examples: "L-tryptophan", "pyruvate", "Mn+2"

Select one or more evidence codes to filter the result to only include gene products that have the corresponding evidence for their function. Deselecting all evidence codes has the same effect as selecting all evidence codes -- no filtering will be done based on evidence code.

Well characterized:

Extensive direct experimental characterization, mechanistic knowledge of phenotype and molecular function.

Partially characterized:

Sequence similarity to a characterized protein, PFAM hit to a domain of known function, and/or partial experimental characterization.

Uncharacterized:

Very little is known. Sequence analysis provides little or no information (e.g., hit to PFAM domain of unknown function).

Check one or more boxes to filter the result to only include genes with one of the checked levels of characterization. This information is available for EcoCyc only.

Select one or more cell components to filter the result to only include gene products that have been assigned to those components. Note that not all proteins have been assigned to cell components. Deselecting all cell components has the same effect as selecting all cell components -- no filtering will be done based on cellular location.

Type in a GO term name or ID, browse GO to a particular gene product, or select one or more GO terms to filter your query to only retrieve gene products annotated with that term or terms. Only terms that have gene products annotated to them in this organism are available. If the Gene-Ontology-Terms class above has no children, then this organism lacks any GO annotations. To only include GO terms annotated with a particular evidence code, select one or more evidence codes. If no evidence codes are selected, then no filtering will be done based on evidence.

Type in or browse for an organism

Type in an organism name or NCBI Taxonomy ID, or browse the NCBI Taxonomy to select one or more organisms or organism classes. The results will be filtered to only include genes and products belonging those organisms. Organisms that are not present in the list have no gene products curated for them. Deselecting all organisms has the same effect as selecting all organisms -- no filtering will be done based on organism.

PubMed ID:
Author:
Title:

Enter a PubMed ID, an author last name, and/or part of an article title in order to find genes and gene products that cite the corresponding publication or author.

If multiple feature types are specified, return proteins that have of the specified types.

Select one or more protein feature types to filter the result to only include gene products for which features of those types have been identified. If no feature classes are listed, this database does not contain protein feature data.

Specify List of Organism Databases

Organism Filter:

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Search for taxon in taxonomy tree:

Find organism databases according to:

Organism characteristics, e.g. pathogenicity = human
Collection metadata, e.g. human microbiome body site = blood
Database properties, e.g. # (number) of Genes < 500

Database lists include both predefined lists and lists that are saved as SmartTables that you can edit from your My SmartTables page. To add all organisms from a saved list, check the box next to the list name and then click the "Add" button.

You have no saved database lists

Tier 1 and Tier 2 databases are displayed with orange and blue backgrounds, respectively.

Current Selection

0 databases or taxa currently selected.

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Note: if you create a user account and log in, you can save your database lists for next time.

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