3. Click on “Details” for A. thaliana. You will be taken to a new
page that displays experimental details about ABI3 in
A. thaliana. For instance, you can see under the “Sequence”
section of the page that there are three serines and two threonines that were found to be phosphorylated (see Fig. 21). If we
click on any of these amino acids, we will be taken to new page
displaying additional experimental details about how this peptide fragment was identified. If we did not know that phosphorylation of our protein of interest was important for its
regulation, as is the case for ABI3 [61], we could hypothesize
that posttranslational modification is important for its
regulation.
3.9.4 Plant PTM Viewer
Similar to P
3 DB, Plant PTM Viewer is an integrative, centralized
database of proteomics-detected posttranslational modifications
(PTMs), such as phosphorylation sites, in many plant proteins.
Unlike P
3
DB, Plant PTM Viewer contains data describing other
PTMs such as, but not limited to, methylation, nitrosylation, ubiquitination, and glycosylation [62]. In total, 37,000 PTM sites are
reported for five different plant species, including Arabidopsis.
Plant PTM Viewer is also an open repository of published data
sets; therefore the limiting factor on data availability is what has
been published. Plant PTM Viewer also contains detailed and
comprehensive tutorials for site utility, which can be found here:
https://dev.bits.vib.be/ptm-viewer/tutorial.php.
Fig. 21 Portion of P
3
DB output for ABI3
Arabidopsis Bioinformatics
67
page that displays experimental details about ABI3 in
A. thaliana. For instance, you can see under the “Sequence”
section of the page that there are three serines and two threonines that were found to be phosphorylated (see Fig. 21). If we
click on any of these amino acids, we will be taken to new page
displaying additional experimental details about how this peptide fragment was identified. If we did not know that phosphorylation of our protein of interest was important for its
regulation, as is the case for ABI3 [61], we could hypothesize
that posttranslational modification is important for its
regulation.
3.9.4 Plant PTM Viewer
Similar to P
3 DB, Plant PTM Viewer is an integrative, centralized
database of proteomics-detected posttranslational modifications
(PTMs), such as phosphorylation sites, in many plant proteins.
Unlike P
3
DB, Plant PTM Viewer contains data describing other
PTMs such as, but not limited to, methylation, nitrosylation, ubiquitination, and glycosylation [62]. In total, 37,000 PTM sites are
reported for five different plant species, including Arabidopsis.
Plant PTM Viewer is also an open repository of published data
sets; therefore the limiting factor on data availability is what has
been published. Plant PTM Viewer also contains detailed and
comprehensive tutorials for site utility, which can be found here:
https://dev.bits.vib.be/ptm-viewer/tutorial.php.
Fig. 21 Portion of P
3
DB output for ABI3
Arabidopsis Bioinformatics
67