13. Definition of functional classifications¶
While the SEED project is a living annotation system, Sequedex, by necessity, used a snapshot of this system that was frozen in September of 2011 in its functional module seed_0911, distributed by default in its first data modules. In this chapter, we define the various subsystems. The ‘si’ number is used only by Sequedex, and does not have meaning at theSEED.org beyond that presented in this table. They are grouped by high-level rollup category. Most of the subsystems should be available at http://pubseed.theseed.org/seedviewer.cgi?page=SubsystemSelect.
13.1. Amino Acids and Derivatives¶
13.2. Carbohydrates¶
13.3. Cell Division and Cell Cycle¶
si_# | category | subsystem |
---|---|---|
0153 | Unclassified cell division | Bacterial_Cytoskeleton |
0154 | Control_of_cell_elongation__division_cycle_in_Bacilli |
|
0155 | Cyanobacterial_Circadian_Clock |
|
0156 | Heterocyst_formation_in_cyanobacteria |
|
0157 | Intracellular_septation_in_Enterobacteria |
|
0158 | Macromolecular_synthesis_operon |
|
0159 | MukBEF_Chromosome_Condensation |
|
0160 | Two_cell_division_clusters_relating_to_chromosome_partitioning |
|
0161 | YgjD_and_YeaZ |
13.4. Cell Wall and Capsule¶
13.5. Clustering-based subsystems¶
13.6. Cofactors, Vitamins, Prosthetic Groups, Pigments¶
13.7. DNA Metabolism¶
13.8. Dormancy and Sporulation¶
si_# | category | subsystem |
---|---|---|
0431 | Spore DNA protection | Dipicolinate_Synthesis |
0432 | Small_acid-soluble_spore_proteins |
|
0433 | Unclassified | Bacillus_Sporulation_Killing_Factor_A_Biosynthetic_Cluster |
0434 | Bacillus_biofilm_matrix_protein_component_TasA_and_homologs |
|
0435 | Exosporium |
|
0436 | Persister_Cells |
|
0437 | SpoVS_protein_family |
|
0438 | Spore_Core_Dehydration |
|
0439 | Spore_germination |
|
0440 | Spore_pigment_biosynthetic_cluster_in_Actinomycetes |
|
0441 | Sporulation-associated_proteins_with_broader_functions |
|
0442 | Sporulation_Cluster_III_A |
|
0443 | Sporulation_draft |
|
0444 | Sporulation_gene_orphans |
13.9. Fatty Acids, Lipids, and Isoprenoids¶
si_# | category | subsystem |
---|---|---|
0445 | Fatty acids | Acyl-CoA_thioesterase_II |
0446 | Carnitine_Metabolism_in_Microorganisms |
|
0447 | Fatty_Acid_Biosynthesis_FASI |
|
0448 | Fatty_Acid_Biosynthesis_FASII |
|
0449 | Fatty_acid_degradation_regulons |
|
0450 | Phospholipid_and_Fatty_acid_biosynthesis_related_cluster |
|
0451 | Polyunsaturated_Fatty_Acids_synthesis |
|
0452 | Isoprenoids | Acyclic_terpenes_utilization |
0453 | Archaeal_lipids |
|
0454 | Carotenoids |
|
0455 | Isoprenoid_Biosynthesis |
|
0456 | Myxoxanthophyll_biosynthesis_in_Cyanobacteria |
|
0457 | Polyprenyl_Diphosphate_Biosynthesis |
|
0458 | polyprenyl_synthesis |
|
0459 | Phospholipids | Glycerolipid_and_Glycerophospholipid_Metabolism_in_Bacteria |
0460 | Sphingolipid_biosynthesis |
|
0461 | Triacylglycerols | Triacylglycerol_metabolism |
0462 | Unclassified | Cholesterol_catabolic_operon_in_Mycobacteria |
0463 | Polyhydroxybutyrate_metabolism |
13.10. Iron acquisition and metabolism¶
si_# | category | subsystem |
---|---|---|
0464 | Siderophores | Alcaligin_Siderophore |
0465 | Bacillibactin_Siderophore |
|
0466 | Iron_siderophore_sensor_&_receptor_system |
|
0467 | Petrobactin-mediated_iron_uptake_system |
|
0468 | Salmochelin-mediated_Iron_Acquisition |
|
0469 | Siderophore_Achromobactin |
|
0470 | Siderophore_Aerobactin |
|
0471 | Siderophore_Desferrioxamine_E |
|
0472 | Siderophore_Enterobactin |
|
0473 | Siderophore_Pyoverdine |
|
0474 | Siderophore_Staphylobactin |
|
0475 | Siderophore_Yersiniabactin_Biosynthesis |
|
0476 | Siderophore_[Alcaligin-like] |
|
0477 | Siderophore_assembly_kit |
|
0478 | Siderophore_pyochelin |
|
0479 | Vibrioferrin_synthesis |
|
0480 | Unclassified | Campylobacter_Iron_Metabolism |
0481 | Ferrous_iron_transporter_EfeUOB,_low-pH-induced |
|
0482 | Heme,_hemin_uptake_and_utilization_systems_in_GramPositives |
|
0483 | Hemin_transport_system |
|
0484 | Iron_Scavenging_cluster_in_Thermus |
|
0485 | Iron_acquisition_in_Streptococcus |
|
0486 | Iron_acquisition_in_Vibrio |
|
0487 | Transport_of_Iron |
13.11. Membrane Transport¶
13.12. Metabolism of Aromatic Compounds¶
13.13. Miscellaneous¶
si_# | category | subsystem |
---|---|---|
0564 | Plant-Prokaryote DOE | At2g33980_At1g28960 |
. | project | |
0565 | At3g21300 |
|
0566 | COG2363 |
|
0567 | Conserved_gene_cluster_possibly_involved_in_RNA_metabolism |
|
0568 | Iojap |
|
0569 | Synechocystis_experimental |
|
0570 | Unclassified | Archease |
0571 | Archease2 |
|
0572 | Broadly_distributed_proteins_not_in_subsystems |
|
0573 | Luciferases |
|
0574 | Magnetosome_Biomineralization_and_Function |
|
0575 | Muconate_lactonizing_enzyme_family |
|
0576 | YaaA |
|
0577 | YbbK |
|
0578 | ZZ_gjo_need_homes |
13.14. Motility and Chemotaxis¶
si_# | category | subsystem |
---|---|---|
0579 | Flagellar motility in | Additional_flagellar_genes_in_Vibrionales |
. | Prokaryota | |
0580 | Archaeal_Flagellum |
|
0581 | Flagellar_motility |
|
0582 | Flagellum |
|
0583 | Flagellum_in_Campylobacter |
|
0584 | Social motility and | Control_of_Swarming_in_Vibrio_and_Shewanella_species |
. | nonflagellar swimming | |
. | in bacteria | |
0585 | Rhamnolipids_in_Pseudomonas |
|
0586 | Unclassified | Bacterial_Chemotaxis |
13.15. Nitrogen Metabolism¶
si_# | category | subsystem |
---|---|---|
0587 | Unclassified | Allantoin_Utilization |
0588 | Amidase_clustered_with_urea_and_nitrile_hydratase_functions |
|
0589 | Ammonia_assimilation |
|
0590 | Cyanate_hydrolysis |
|
0591 | Denitrification |
|
0592 | Dissimilatory_nitrite_reductase |
|
0593 | Nitrate_and_nitrite_ammonification |
|
0594 | Nitric_oxide_synthase |
|
0595 | Nitrogen_fixation |
|
0596 | Nitrosative_stress |
13.16. Nucleosides and Nucleotides¶
si_# | category | subsystem |
---|---|---|
0597 | Detoxification | Housecleaning_nucleoside_triphosphate_pyrophosphatases |
0598 | Nucleoside_triphosphate_pyrophosphohydrolase_MazG |
|
0599 | Nudix_proteins_(nucleoside_triphosphate_hydrolases) |
|
0600 | Purines | De_Novo_Purine_Biosynthesis |
0601 | Purine_Utilization |
|
0602 | Purine_conversions |
|
0603 | Purine_nucleotide_synthesis_regulator |
|
0604 | Xanthine_Metabolism_in_Bacteria |
|
0605 | Xanthosine_utilization_(xap_region) |
|
0606 | Pyrimidines | De_Novo_Pyrimidine_Synthesis |
0607 | Novel_non-oxidative_pathway_of_Uracil_catabolism |
|
0608 | Pyrimidine_utilization |
|
0609 | pyrimidine_conversions |
|
0610 | Unclassified | AMP_to_3-phosphoglycerate |
0611 | Adenosyl_nucleosidases |
|
0612 | Hydantoin_metabolism |
|
0613 | Pseudouridine_Metabolism |
|
0614 | Ribonucleotide_reduction |
13.17. Phages, Prophages, Transposable elements, Plasmids¶
si_# | category | subsystem |
---|---|---|
0615 | Bacteriophage integration | Phage_integration_and_excision |
. | /excision/lysogeny | |
0616 | Bacteriophage structural | Phage_capsid_proteins |
. | proteins | |
0617 | Superinfection Exclusion | Phage_Dual_Exonuclease_Exclusion |
0618 | Pathogenicity islands | Listeria_Pathogenicity_Island_LIPI-1_extended |
0619 | Staphylococcal_pathogenicity_islands_SaPI |
|
0620 | Vibrio_pathogenicity_island |
|
0621 | Phages, Prophages | Listeria_phi-A118-like_prophages |
0622 | Phage_baseplate_proteins |
|
0623 | Phage_neck_proteins |
|
0624 | Phage_nin_genes_-_N-independent_survival |
|
0625 | Phage_packaging_machinery |
|
0626 | Phage_tail_fiber_proteins |
|
0627 | Phage_tail_proteins_2 |
|
0628 | Prophage-encoded_Rst_operon |
|
0629 | Prophage_lysogenic_conversion_modules |
|
0630 | Staphylococcal_phi-Mu50B-like_prophages |
|
0631 | Plasmid related functions | Plasmid-encoded_T-DNA_transfer |
0632 | Rolling-circle_replication |
|
0633 | Transposable elements | CBSS-203122.12.peg.188 |
0634 | Conjugative_transposon,_Bacteroidales |
|
0635 | Tn552 |
|
0636 | Unclassified | Integrons |
13.18. Phosphorous Metabolism¶
si_# | category | subsystem |
---|---|---|
0637 | Unclassified | Alkylphosphonate_utilization |
0638 | High_affinity_phosphate_transporter_and_control_of_PHO_regulon |
|
0639 | P_uptake_(cyanobacteria) |
|
0640 | Phosphate_metabolism |
|
0641 | Phosphoenolpyruvate_phosphomutase |
|
0642 | Phosphonate_metabolism |
13.19. Photosynthesis¶
si_# | category | subsystem |
---|---|---|
0643 | Electron transport and | Photosystem_I |
. | photophosphorylation | |
0644 | Photosystem_I-type_photosynthetic_reaction_center |
|
0645 | Photosystem_II |
|
0646 | Photosystem_II-type_photosynthetic_reaction_center |
|
0647 | Light-harvesting complexes | Bacterial_light-harvesting_proteins |
0648 | Chlorosome |
|
0649 | Phycobilisome |
|
0650 | Unclassified | Bacteriorhodopsin |
0651 | Proteorhodopsin |
13.20. Potassium metabolism¶
si_# | category | subsystem |
---|---|---|
0652 | Unclassified | Glutathione-regulated_potassium-efflux_system_and_associated_functions |
0653 | Hyperosmotic_potassium_uptake |
|
0654 | Potassium_homeostasis |
|
0655 | pH_adaptation_potassium_efflux_system |
13.21. Protein Metabolism¶
13.22. RNA Metabolism¶
13.23. Regulation and Cell signaling¶
13.24. Respiration¶
13.25. Secondary Metabolism¶
si_# | category | subsystem |
---|---|---|
0827 | Aromatic amino acids and | Cinnamic_Acid_Degradation |
. | derivatives | |
0828 | Bacterial cytostatics, | 2-isocapryloyl-3R-hydroxymethyl-gamma-butyrolactone_and_other_bacterial_morphogens |
. | differentiation factors and | |
. | antibiotic | |
0829 | Clavulanic_acid_biosynthesis |
|
0830 | Nonribosomal_peptide_synthetases_(NRPS)_in_Frankia_sp._Ccl3 |
|
0831 | Paerucumarin_Biosynthesis |
|
0832 | Phenazine_biosynthesis |
|
0833 | Biologically active compounds | Steroid_sulfates |
. | in metazoan cell defence and | |
. | differentiation | |
0834 | Biosynthesis of | Apigenin_derivatives |
. | phenylpropanoids | |
0835 | Biflavanoid_biosynthesis |
|
0836 | Caffeic_acid_derivatives |
|
0837 | Flavanone_biosynthesis |
|
0838 | Phenylpropionate_Degradation |
|
0839 | Tannin_biosynthesis |
|
0840 | Plant Alkaloids | Alkaloid_biosynthesis_from_L-lysine |
0841 | Plant Hormones | Auxin_biosynthesis |
0842 | Auxin_degradation |
13.26. Stress Response¶
13.27. Sulfur Metabolism¶
si_# | category | subsystem |
---|---|---|
0881 | Inorganic sulfur | Inorganic_Sulfur_Assimilation |
. | assimilation | |
0882 | Organic sulfur assimilation | Alkanesulfonate_assimilation |
0883 | Alkanesulfonates_Utilization |
|
0884 | DMSP_breakdown |
|
0885 | L-Cystine_Uptake_and_Metabolism |
|
0886 | Taurine_Utilization |
|
0887 | Utilization_of_glutathione_as_a_sulphur_source |
|
0888 | Unclassified | Dimethylsulfoniopropionate_(DMSP)_mineralization |
0889 | Galactosylceramide_and_Sulfatide_metabolism |
|
0890 | Release_of_Dimethyl_Sulfide_(DMS)_from_Dimethylsulfoniopropionate_(DMSP) |
|
0891 | Sulfate_reduction-associated_complexes |
|
0892 | Sulfur_oxidation |
|
0893 | Thioredoxin-disulfide_reductase |