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.
Find out all about SUBA4
Find the SUBA4 Tutorial Page
Cite SUBA using the citation guide
SUBA4 Notice board
!!Coming Soon: We are updating SUBA to include experimental localisation up to 2020.
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 2017.
SUBAcon was last retrained using data up to: 30th June 2017.
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
Bit Score is log2Neff-log2(E-value)
where E-value = pval × Neff
is the p-value times the
effective search space size. The larger the bit-score the better since
pval = P(random seq having a better score) = 2-(bit-score)
. 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. Multiplying by the number of possible matches
gives the e-value
or the expected number of hits with a better match just by random chance.
(See here).
Bit Score is log2Neff-log2(E-value)
where E-value = pval × Neff
is the p-value times the
effective search space size. The larger the bit-score the better since
pval = P(random seq having a better score) = 2-(bit-score)
. 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. Multiplying by the number of possible matches
gives the e-value
or the expected number of hits with a better match just by random chance.
(See here).
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)