PPDB

The Plastid Proteome Database

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PPDB home page

Browse MapMan Bins**:

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)
1.1 PS.lightreaction (965)
1.2 PS.photorespiration (119)
1.3 PS.calvin cyle (229)
1.4 PS.reductive PP (0)
2 major CHO metabolism (526)
2.1 major CHO metabolism.synthesis (201)
2.2 major CHO metabolism.degradation (325)
3 minor CHO metabolism (549)
3.1 minor CHO metabolism.raffinose family (59)
3.2 minor CHO metabolism.trehalose (83)
3.3 minor CHO metabolism.sugar alcohols (12)
3.4 minor CHO metabolism.myo-inositol (64)
3.5 minor CHO metabolism.others (241)
3.6 minor CHO metabolism.callose (35)
3.7 minor CHO metabolism.sugar kinases (8)
3.8 minor CHO metabolism.galactose (47)
4 glycolysis (442)
5 fermentation (84)
6 gluconeogenese/ glyoxylate cycle (47)
7 OPP (123)
7.1 OPP.oxidative PP (74)
7.2 OPP.non-reductive PP (37)
7.3 OPP.electron transfer (12)
8 TCA / org. transformation (450)
9 mitochondrial electron transport / ATP synthesis (563)
10 cell wall (1557)
10.1 cell wall.precursor synthesis (210)
10.2 cell wall.cellulose synthesis (182)
10.3 cell wall.hemicellulose synthesis (87)
10.4 cell wall.pectin synthesis (5)
10.5 cell wall.cell wall proteins (230)
10.6 cell wall.degradation (356)
10.7 cell wall.modification (298)
10.8 cell wall.pectin*esterases (181)
11 lipid metabolism (1611)
12 N-metabolism (136)
13 amino acid metabolism (1373)
13.1 amino acid metabolism.synthesis (962)
13.2 amino acid metabolism.degradation (395)
13.99 amino acid metabolism.misc (6)
14 S-assimilation (84)
15 metal handling (220)
16 secondary metabolism (1514)
16.1 secondary metabolism.isoprenoids (465)
16.2 secondary metabolism.phenylpropanoids (433)
16.3 secondary metabolism.shikimate pathway (0)
16.4 secondary metabolism.N misc (88)
16.5 secondary metabolism.sulfur-containing (36)
16.7 secondary metabolism.wax (86)
16.8 secondary metabolism.flavonoids (339)
16.10 secondary metabolism.simple phenols (51)
16.99 secondary metabolism.unspecified (16)
17 hormone metabolism (1567)
17.1 hormone metabolism.abscisic acid (193)
17.2 hormone metabolism.auxin (473)
17.3 hormone metabolism.brassinosteroid (224)
17.4 hormone metabolism.cytokinin (95)
17.5 hormone metabolism.ethylene (287)
17.6 hormone metabolism.gibberelin (127)
17.7 hormone metabolism.jasmonate (131)
17.8 hormone metabolism.salicylic acid (37)
18 Co-factor and vitamine metabolism (237)
18.1 Co-factor and vitamine metabolism.molybdenum cofactor (19)
18.2 Co-factor and vitamine metabolism.thiamine (33)
18.3 Co-factor and vitamine metabolism.riboflavin (39)
18.4 Co-factor and vitamine metabolism.pantothenate (22)
18.5 Co-factor and vitamine metabolism.folate & vitamine K (32)
18.6 Co-factor and vitamine metabolism.biotin (14)
18.8 Co-factor and vitamine metabolism.ubiquinone (7)
18.9 Co-factor and vitamine metabolism.vitamin E (0)
18.10 Co-factor and vitamine metabolism.coenzyme M (0)
18.11 Co-factor and vitamine metabolism.lipoic acid (12)
18.13 Co-factor and vitamine metabolism.isochorismatase (5)
18.20* Co-factor and vitamine metabolism.vitamin b6 (12)
18.21* Co-factor and vitamine metabolism.NAD/NADP (12)
19 tetrapyrrole synthesis (263)
20 stress (2716)
21 redox.regulation (930)
22 polyamine metabolism (73)
23 nucleotide metabolism (680)
23.1 nucleotide metabolism.synthesis (172)
23.2 nucleotide metabolism.degradation (160)
23.3 nucleotide metabolism.salvage (87)
23.4 nucleotide metabolism.phosphotransfer and pyrophosphatases (209)
23.5 nucleotide metabolism.deoxynucleotide metabolism (46)
23.6 nucleotide metabolism.signalling (0)
24 Biodegradation of Xenobiotics (94)
24.1 Biodegradation of Xenobiotics.hydroxyacylglutathione hydrolase (20)
24.2 Biodegradation of Xenobiotics.lactoylglutathione lyase (59)
24.3 Biodegradation of Xenobiotics.3-hydroxybutyryl-CoA dehydrogenase (3)
25 C1-metabolism (141)
25.1 C1-metabolism.glycine hydroxymethyltransferase (22)
25.2 C1-metabolism.formate-tetrahydrofolate ligase (8)
25.3 C1-metabolism.dihydropteridine diphosphokinase (5)
25.4 C1-metabolism.5-formyltetrahydrofolate cyclo-ligase (7)
25.5 C1-metabolism.Methylenetetrahydrofolate dehydrogenase & Methenyltetrahydrofolate cyclohydrolase (21)
25.6 C1-metabolism.methylenetetrahydrofolate reductase (8)
25.7 C1-metabolism.GTP cyclohydrolase I (4)
25.8 C1-metabolism.tetrahydrofolate synthase (13)
25.9 C1-metabolism.dihydroneopterin aldolase (9)
25.10 C1-metabolism.formate dehydrogenase (13)
25.11 C1-metabolism.S-(hydroxymethyl)glutathione dehydrogenase & S-(hydroxymethyl)glutathione synthase (4)
26 misc (4622)
27 RNA (9846)
28 DNA (1908)
28.1 DNA.synthesis/chromatin structure (1199)
28.2 DNA.repair (304)
28.3* DNA.plastid nucleoid interacting (44)
28.5* DNA.DEAD BOX helicase (1)
28.99 DNA.unspecified (361)
29 protein (14276)
29.1 protein.aa activation (391)
29.2 protein.synthesis (3287)
29.3 protein.targeting (1107)
29.4 protein.postranslational modification (2724)
29.5 protein.degradation (6003)
29.6 protein.folding (492)
29.7 protein.glycosylation (114)
29.8 protein assembly and cofactor ligation (121)
29.9* protein. processing (13)
30 signalling (4010)
31 cell (2769)
33 development (2016)
33.1 development.storage proteins (85)
33.2 development.late embryogenesis abundant (70)
33.30 development.multitarget (8)
33.99 development.unspecified (1850)
34 transport (3437)
35 not assigned (27188)
35.1 not assigned.no ontology (10876)
35.2 not assigned.unknown (16334)

Display options:
STD Annot.Lab Annot.Curated Loc.TAIR Loc.MapManBin
sep.MapManBinAramemnonTMHMMTargetPPredotar
PFAMCysCalc.gravyCalc.MWCalc.PI
exp.MW_dexp.pI_dexp.MW_nexp.pI_nexp.Volume
exp.ambiguityexp.amb_gmodelexp.relatedexp.MS_typeexp.MascotScore
exp.#peptidesexp.ID*exp.spotexp.queriesexp.uniq.queries
exp.adjusted.queriesexp.Tissueexp.Genotypeexp.Sep.StepsCellType
ProteomicsPub.GFP/YFP loc.Best AT hitBest Rice hitBest Maize hit
CoverageTop3pepTop3pep(-MetCys)#Tryptic Frag.#Tryptic Frag.(-ctp)
#Tryptic Frag.(-ltp)    

*exp.ID: Details of the experimental sources.

Output: 

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.)


©Klaas J. van Wijk Lab, Cornell University