PPDB

PPDB	The Plastid Proteome Database

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PPDB home page

Browse MapMan Bins**:

If checked, only show proteins that are experimentally identified in van Wijk lab

Instructions:

Click "+" button to expand a bin, click "-" button to shrink a bin

The number next to the bin name is the number of gene models within a bin. Click the number to retrieve genes

To customize the output results, you can use the panel below to define the display columns

** The MapMan annotations are provided by Thimm et al. (Thimm O, Blasing O, Gibon Y, Nagel A, Meyer S, Kruger P, Selbig J, Muller LA, Rhee SY, Stitt M. (2004) MAPMAN: a user-driven tool to display genomics data sets onto diagrams of metabolic pathways and other biological processes. Plant J. 37:914-39)

The bin assignment for a number of proteins were changed by the ''van Wijk lab' based on experimental proteomics information, as well as information from published literature. Also, a small number of additional Bins were created to accommodate more precise functional assignment - These new Bins are marked with an asterix (*).

1 PS (1313)
2 major CHO metabolism (526)
3 minor CHO metabolism (549)
4 glycolysis (442)
5 fermentation (84)
6 gluconeogenese/ glyoxylate cycle (47)
7 OPP (123)
8 TCA / org. transformation (450)
9 mitochondrial electron transport / ATP synthesis (563)
10 cell wall (1557)
11 lipid metabolism (1611)
12 N-metabolism (136)
13 amino acid metabolism (1373)
14 S-assimilation (84)
15 metal handling (220)
16 secondary metabolism (1514)
17 hormone metabolism (1567)
18 Co-factor and vitamine metabolism (237)
19 tetrapyrrole synthesis (263)
20 stress (2716)
21 redox.regulation (930)
22 polyamine metabolism (73)
23 nucleotide metabolism (680)
24 Biodegradation of Xenobiotics (94)
25 C1-metabolism (141)
26 misc (4622)
27 RNA (9846)
28 DNA (1908)
29 protein (14276)
30 signalling (4010)
31 cell (2769)
33 development (2016)
34 transport (3437)
35 not assigned (27188)

Display options:

STD Annot. Lab Annot. Curated Loc. TAIR Loc. MapManBin
sep.MapManBin Aramemnon TMHMM TargetP Predotar
PFAM Cys Calc.gravy Calc.MW Calc.PI
exp.MW_d exp.pI_d exp.MW_n exp.pI_n exp.Volume
exp.ambiguity exp.amb_gmodel exp.related exp.MS_type exp.MascotScore
exp.#peptides exp.ID* exp.spot exp.queries exp.uniq.queries
exp.adjusted.queries exp.Tissue exp.Genotype exp.Sep.Steps CellType
ProteomicsPub. GFP/YFP loc. Best AT hit Best Rice hit Best Maize hit
Coverage Top3pep Top3pep(-MetCys) #Tryptic Frag. #Tryptic Frag.(-ctp)
#Tryptic Frag.(-ltp)

*exp.ID: Details of the experimental sources.

Output: webexcel file

Restrict species:

Species

Source of sequence:

Extra options:

Experiments Spots
(enter experiment IDs separated by space. Check the list if you do not know the IDs.)