Protein location inferred by to be in
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Add
Search for proteins that have (or have not) been assigned to a specific subcellular location by direct assay.
GFP and MSMS describe assignments that were made by local curators based on in-house research or literature survey.
TAIR, UniProt and AmiGO describe assignments made by external curators based on direct assay evidence.
Protein location predicted by to be in
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Add
Search for proteins that have (or have not) been assigned to a specific subcellular location by a
predictor program. Assignments are based on the protein set from TAIR7 and include the following
predictors: iPSORT, WoLF PSORT, Mitopred, MitoProt2, SubLoc, PeroxP, Predotar, TargetP
Protein location described in
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Add
One aspect of SUBA involved manual literature trawling for papers related to subcellular
protein localization in Arabidopsis. Use this query component to extract calls by referenced paper.
If you know of a paper that does not appear to be in the list, please inform Harvey Millar
(hmillar(at)cyllene.uwa.edu.au) or Joshua Heazlewood (botjlh(at)cyllene.uwa.edu.au).
Protein information keyword
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Add
Search for/exclude proteins by keyword. A search will be conducted against the TAIR description of
proteins in the SUBA database. The syntax of this search supports extended regular expressions (see
this site for more information)
Numeric options:
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Add
Filter for proteins based on various numeric data, derived from TAIR7 or calculated locally.
Underlying gene model chromosome
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Add
Filter proteins so that only those that are translated from genes on (or not on) the specified chromosome
are included
Arabidopsis Gene Identifier ↓Add
Enter a list of valid AGI's separated by new lines, spaces, commas, tabs or semi-colons. Alternative splice
information may be included if desired. The search will attempt to filter results based on the list you
have provided
SUBA version 2.2
The SubCellular Proteomic Database (SUBA) houses large scale proteomic and GFP localisation sets from cellular
compartments of Arabidopsis. It also contains precompiled bioinformatic predictions for protein subcellular
localisations. SUBA was last updated in October 2007 and is based on the TAIR7 genome annotation release.
A PDF tutorial explaining how to use SUBA is available here: SUBA tutorial.
If you find this resource useful please cite one of the following publications:
Heazlewood JL, Verboom RE, Tonti-Filippini J, Small I and Millar AH. (2007) SUBA: the Arabidopsis Subcellular Database. Nucleic Acids Res.35:D213-D218. (PubMed)
Heazlewood JL, Tonti-Filippini J, Verboom RE, Millar AH. (2005) Combining experimental and predicted datasets for determination of the subcellular location of proteins in Arabidopsis. Plant Physiol.139(2):598-609. (PubMed)
