Difference between revisions of "Sandbox"

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'''All genes are grouped in one or more categories. These categories help to identify genes/proteins with common function, regulation or properties.
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To see additional subcategories, please go to the pages for the six top-level categories.
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'''
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==1. [[Cellular processes]]==
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* 1.1. Cell envelope and cell division
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** 1.1.1. [[Cell wall synthesis]]
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** 1.1.2. [[Cell shape]]
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** 1.1.3. [[Cell wall degradation/ turnover]]
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** 1.1.4. [[Capsule biosynthesis and degradation]]
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** 1.1.5. [[Cell wall/ other]]
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** 1.1.6. [[Membrane dynamics]]
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** 1.1.7. [[Cell division]]
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* 1.2. Transporters
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** 1.2.1. [[ABC transporters]]
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** 1.2.2. [[Phosphotransferase systems]]
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** 1.2.3. [[Transporters/ other]]
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* 1.3. Homeostasis
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** 1.3.1. [[Metal ion homeostasis (K, Na, Ca, Mg)]]
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** 1.3.2. [[Trace metal homeostasis (Cu, Zn, Ni, Mn, Mo)]]
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** 1.3.3. [[Acquisition of iron]]
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** 1.3.4. [[pH homeostasis]]
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==2. [[Metabolism]]==
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* 2.1. Electron transport and ATP synthesis
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** 2.1.1. [[Regulators of electron transport]]
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** 2.1.2. [[Respiration]]
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** 2.1.3. [[Electron transport/ other]]
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** 2.1.4. [[ATP synthesis]]
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* 2.2. Carbon metabolism
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** 2.2.1. [[Carbon core metabolism]]
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** 2.2.2. [[Utilization of specific carbon sources]]
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* 2.3. Amino acid/ nitrogen metabolism
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** 2.3.1. [[Biosynthesis/ acquisition of amino acids]]
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** 2.3.2. [[Utilization of amino acids]]
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** 2.3.3. [[Utilization of nitrogen sources other than amino acids]]
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** 2.3.4. [[Putative amino acid transporter]]
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* 2.4. Lipid metabolism
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** 2.4.1. [[Utilization of lipids]]
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** 2.4.2. [[Biosynthesis of lipids]]
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** 2.4.3. [[Lipid metabolism/ other]]
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* 2.5. Nucleotide metabolism
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** 2.5.1. [[Utilization of nucleotides]]
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** 2.5.2. [[Biosynthesis/ acquisition of nucleotides]]
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** 2.5.3. [[Metabolism of signalling nucleotides]]
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** 2.5.4. [[Nucleotide metabolism/ other]]
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* 2.6. Additional metabolic pathways
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** 2.6.1. [[Biosynthesis of cell wall components]]
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** 2.6.2. [[Biosynthesis of cofactors]]
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** 2.6.3. [[Phosphate metabolism]]
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** 2.6.4. [[Sulfur metabolism]]
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** 2.6.5. [[Iron metabolism]]
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** 2.6.6. [[Miscellaneous metabolic pathways]]
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==3. [[Information processing]]==
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* 3.1. Genetics
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** 3.1.1. [[DNA replication]]
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** 3.1.2. [[DNA condensation/ segregation]]
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** 3.1.3. [[DNA restriction/ modification]]
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** 3.1.4. [[DNA repair/ recombination]]
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** 3.1.5. [[Genetic competence]]
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** 3.1.6. [[Genetics/ other]]
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* 3.2. RNA synthesis and degradation
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** 3.2.1. [[Transcription]]
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** 3.2.2. [[RNA chaperones]]
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** 3.2.3. [[DEAD-box RNA helicases]]
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** 3.2.4. [[RNases]]
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* 3.3. Protein synthesis, modification and degradation
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** 3.3.1. [[Translation]]
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** 3.3.2. [[Chaperones/ protein folding]]
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** 3.3.3. [[Protein modification]]
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** 3.3.4. [[Protein secretion]]
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** 3.3.5. [[Proteolysis]]
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* 3.4. Regulation of gene expression
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** 3.4.1. [[Sigma factors and their control]]
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**''' 3.4.2. [[Two-component regulatory systems and their control]]'''
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**''' 3.4.3. [[DNA binding transcription factors and their control]]'''
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** 3.4.4. [[Trigger enzymes]]
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**''' 3.4.5. [[PRD-type regulators]]'''
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** 3.4.6. [[RNA binding regulators]]
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==4. [[Lifestyles]]==
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* 4.1. Exponential and early post-exponential lifestyles
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** 4.1.1. [[Motility and chemotaxis]]
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** 4.1.2. [[Biofilm formation]]
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** 4.1.3. [[Genetic competence]]
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**''' 4.1.4. [[Transition state regulators]]'''
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**''' 4.1.5. [[Quorum sensing]]'''
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* 4.2. Sporulation and Germination
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** 4.2.1. [[Sporulation proteins]]
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** 4.2.2. [[Phosphorelay]]
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** 4.2.3. [[Sporulation/ other]]
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** 4.2.4. [[Germination]]
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* 4.3. Coping with stress
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** 4.3.1. [[General stress proteins (controlled by SigB)]]
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** 4.3.2. [[Cell envelope stress proteins (controlled by SigM, W, X, Y)]]
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** 4.3.3. [[Acid stress proteins (controlled by YvrI-YvrHa)]]
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** 4.3.4. [[Heat shock proteins]]
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** 4.3.5. [[Cold stress proteins]]
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** 4.3.6. [[Coping with hyper-osmotic stress]]
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** 4.3.7. [[Coping with hypo-osmotic stress]]
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** 4.3.8. [[Resistance against oxidative and electrophile stress]]
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** 4.3.9. [[Resistance against other toxic compounds (nitric oxide, phenolic acids, flavonoids, oxalate)]]
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** 4.3.10.[[ Resistance against toxic metals]]
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** 4.3.11.[[ Resistance against toxins/ antibiotics]]
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** 4.3.12.[[ Biosynthesis of antibacterial compounds]]
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** 4.3.13.[[ Toxins, antitoxins and immunity against toxins]]
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* 4.4. [[Lifestyles/ miscellaneous]]
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==5. [[Prophages and mobile genetic elements]]==
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* 5.1. Prophages
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** 5.1.1. [[PBSX prophage]]
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** 5.1.2. [[SPß prophage]]
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** 5.1.3. [[Skin element]]
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** 5.1.4. [[Phage-related functions]]
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* 5.2. [[Mobile genetic elements]]
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==6. [[Groups of genes]]==
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* 6.1. [[Essential genes]]
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* 6.2. [[Membrane proteins]]
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* 6.3. [[GTP-binding proteins]]
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* 6.4. [[Phosphoproteins]]
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* 6.5. [[Universally conserved proteins]]
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* 6.6. [[Poorly characterized/ putative enzymes]]
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* 6.7. [[Proteins of unknown function]]
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* 6.8. [[Short peptides]]
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* 6.9. [[ncRNA]]
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* 6.10. [[Pseudogenes]]
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*''' 6.11. [[Regulators of core metabolism]]'''

Revision as of 20:31, 10 September 2011

All genes are grouped in one or more categories. These categories help to identify genes/proteins with common function, regulation or properties.

To see additional subcategories, please go to the pages for the six top-level categories.

1. Cellular processes

2. Metabolism

3. Information processing


4. Lifestyles

5. Prophages and mobile genetic elements

6. Groups of genes

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