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Welcome to SUBA4

What is SUBA?

SUBA is the central resource for Arabidopsis protein subcellular location data. Proteins have specific functions and locations within the plant cell. They generate or are themselves products important for plant growth and response. Protein subcellular location and the proximity relationship of proteins are important clues to function within the metabolic household. Subcellular location can be determined by fluorescent protein tagging or mass spectrometry detection in subcellular purifications and by prediction using protein sequence features.

SUBA provides a subcellular data query platform, protein sequence BLAST alignment, a high confidence subcellular locations reference standards and analytic tools.

SUBA4 Notice board

A description of SUBA4 is now available at Nucleic Acids Res.
Looking for crop protein localisations? Find them at cropPAL for wheat, barley, rice and maize.

NEW data in SUBA4

More localisations and experimental suborganellar localisations and protein-protein interaction localisations
The SUBA4 toolbox for estimating organellar protein abundance (MMAP tool) and protein-protein location relationships (CAT and PAT)

Updates

Bibliographic references were last updated: 30th June 2016.
SUBAcon was last retrained using data up to: 30th June 2016.

Can't find what you are looking for? Email directly to Cornelia Hooper (cornelia.hooper [at] uwa.edu.au)

Try out an instant query for AT2G33210.1

Quick Search

The quick search will search for AGIs in your input as well as search the TAIR descriptions and abstracts of experimental studies for any matching keywords that you provided.

Find the closest Arabidopsis BLAST match to your sequence

Find Arabidopsis proteins that are similar to fragments in the below list with similarity score

Score is -log2(E) where E = pval × Neff is the p-value times the effective search space size. The larger the score the better. i.e. the p-value measures the statistical significance of the match but since we tried Neff times to find a match we need to make a correction. (See here and here [PDF]).

To search for locations of Arabidopsis proteins:
Select a query from below and press the add button beside it (to the right).
To submit a query, click on the  Query button (above).
Find Arabidopsis proteins where the...
... experimental location inferred by to be in
nucleus
matrix | chromatin | nucleolus | envelope | inner membrane | outer membrane
cytosol
ribosomes | cell plate
mitochondrion
envelope | inner membrane | outer membrane | matrix
plastid
envelope | inner membrane | outer membrane | stroma | plastoglobules | thylakoid | lumen | membrane
peroxisome
envelope | matrix
vacuole secretory
membrane | lumen
Golgi secretory
trans-Golgi network | early endosome | multivesicular body | Golgi apparatus | membrane | lumen
extracellular secretory
apoplast | cell wall
endoplasmic reticulum secretory
membrane | lumen
plasma membrane secretory
cytoskeleton
intermediate filament | actin filament | microtubules
with FP image:
... predicted location inferred by to be in
... protein interact with protein(s) in list  
... interacting protein described in
... protein-protein interactions been determined by method of
... interaction experimentally observed in
nucleus
matrix | chromatin | nucleolus | envelope | inner membrane | outer membrane
cytosol
ribosomes | cell plate
mitochondrion
envelope | inner membrane | outer membrane | matrix
plastid
envelope | inner membrane | outer membrane | stroma | plastoglobules | thylakoid | lumen | membrane
peroxisome
envelope | matrix
vacuole secretory
membrane | lumen
Golgi secretory
trans-Golgi network | early endosome | multivesicular body | Golgi apparatus | membrane | lumen
extracellular secretory
apoplast | cell wall
endoplasmic reticulum secretory
membrane | lumen
plasma membrane secretory
cytoskeleton
intermediate filament | actin filament | microtubules
... literature referenced location described by authors (see here for a full list of publications.)
... literature referenced location described in pubmed: ← Must be a PUBMED id
... year of publication of localisation studies is between ←Should be a year and ←Should be a year
... publication title or abstract of the localisation study the keyword(s)
... author's name like
... author's affiliation
... author's affiliation in
... author's afflilation in:

... protein description keyword(s)  
... physical property of is  
... gene model on chromosome
... Arabidopsis Gene Initiative (AGI) identifier(s) in list
... alias, family IDs or protein sequence features the list of identifiers: (e.g. GO:0008270, IPR017986 etc.)
... below protein sequence fragments have BLAST similarity scores

Score is -log2(E) where E = pval × Neff is the p-value times the effective search space size. The larger the score the better. i.e. the p-value measures the statistical significance of the match but since we tried Neff times to find a match we need to make a correction. (See here and here [PDF]).

SUBA4 help menu

How to search SUBA4?

A step-by-step tutorial explaining how to use SUBA4 is available at: SUBA4 tutorials.

How to submit new subcellular localization data to SUBA4?

SUBA is updated annually with the latest update date shown on the home page notice board. If you have published or found data that is not in SUBA please submit this subcellular location data to us. Currently we accept data in the format of PubMedID;location;AGI (e.g. 25900983;golgi;AT5G16280.1). The location categories must be cytoskeleton, cytosol, endoplasmic reticulum, extracellular, golgi, mitochondrion, nucleus, peroxisome, plasma membrane, plastid or vacuole. If you have data fitting these criteria please follow this link: .

We will assess your data and add it to our next scheduled update. If you have suborganellar data for any other location categories or Protein-Protein interaction data, please contact:

  • Cornelia Hooper (cornelia.hooper(at)uwa.edu.au)

Can't get the right data out SUBA4?

If you have specific questions that you cannot pose through the SUBA4 interface, we may be able to help you. We can source, link and combined more types of data than the window to SUBA4 shows. We are open to collaborations and involvement with our users. If you encounter any problems with the SUBA4 interface or find any errors with the data in SUBA4, please contact us:

  • Cornelia Hooper (cornelia.hooper(at)uwa.edu.au)
  • Ian Castleden (ian.castleden(at)uwa.edu.au)
  • Harvey Millar (harvey.millar(at)uwa.edu.au)