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

si_# category subsystem
0000 Alanine, serine, Alanine_biosynthesis
. and glycine  
0001   Glycine_Biosynthesis
0002   Glycine_and_Serine_Utilization
0003   Glycine_cleavage_system
0004   Serine_Biosynthesis
0005 Arginine; urea cycle, Anaerobic_Oxidative_Degradation_of_L-Ornithine
. polyamines .
0006   Arginine_Biosynthesis_extended
0007   Arginine_Deiminase_Pathway
0008   Arginine_and_Ornithine_Degradation
0009   Cyanophycin_Metabolism
0010   Polyamine_Metabolism
0011   Putrescine_utilization_pathways
0012   Urea_decomposition
0013 Aromatic amino acids Aromatic_amino_acid_degradation
. and derivatives  
0014   Aromatic_amino_acid_interconversions_with_aryl_acids
0015   Bacilysin_biosynthesis
0016   Chorismate:_Intermediate_for_synthesis_of_PAPA_antibiotics,_PABA,_anthranilate,_3-hydroxyanthranilate_and_more.
0017   Chorismate_Synthesis
0018   Common_Pathway_For_Synthesis_of_Aromatic_Compounds_(DAHP_synthase_to_chorismate)
0019   Indole-pyruvate_oxidoreductase_complex
0020   Phenylalanine_and_Tyrosine_Branches_from_Chorismate
0021   Tryptophan_catabolism
0022   Tryptophan_synthesis
0023 Branched-chain Branched-Chain_Amino_Acid_Biosynthesis
. amino acids  
0024   Branched_chain_amino_acid_degradation_regulons
0025   HMG_CoA_Synthesis
0026   Isoleucine_degradation
0027   Ketoisovalerate_oxidoreductase
0028   Leucine_Biosynthesis
0029   Leucine_Degradation_and_HMG-CoA_Metabolism
0030   Valine_degradation
0031 Glutamine, glutamate, Glutamate_dehydrogenases
. aspartate, asparagine;  
. ammonia assimilation  
0032   Glutamine,_Glutamate,_Aspartate_and_Asparagine_Biosynthesis
0033   Glutamine_synthetases
0034   Poly-gamma-glutamate_biosynthesis
0035 Histidine Metabolism Histidine_Biosynthesis
0036   Histidine_Degradation
0037 Lysine, threonine, Cysteine_Biosynthesis
. methionine, and cysteine  
0038   Lysine_Biosynthesis_DAP_Pathway
0039   Lysine_biosynthesis_AAA_pathway_2
0040   Lysine_degradation
0041   Lysine_fermentation
0042   Methionine_Biosynthesis
0043   Methionine_Degradation
0044   Methionine_Salvage
0045   Threonine_anaerobic_catabolism_gene_cluster
0046   Threonine_and_Homoserine_Biosynthesis
0047   Threonine_degradation
0048 Proline and A_Hypothetical_Protein_Related_to_Proline_Metabolism
. 4-hydroxyproline  
0049   Proline,_4-hydroxyproline_uptake_and_utilization
0050   Proline_Synthesis
0051 Unclassified amino Creatine_and_Creatinine_Degradation
. acids and derivatives  
0052   L-2-amino-thiazoline-4-carboxylic_acid-Lcysteine_conversion
0053   Phosphonoalanine_utilization

13.2. Carbohydrates

si_# category subsystem
0054 Aminosugars (GlcNAc)2_Catabolic_Operon
0055   Chitin_and_N-acetylglucosamine_utilization
0056   Fructoselysine_(Amadori_product)_utilization_pathway
0057   N-Acetyl-Galactosamine_and_Galactosamine_Utilization
0058   Neotrehalosadiamine_(NTD)_Biosynthesis_Operon
0059 CO2 fixation CO2_uptake,_carboxysome
0060   Calvin-Benson_cycle
0061   Carboxysome
0062   Photorespiration_(oxidative_C2_cycle)
0063 Central carbohydrate Dehydrogenase_complexes
. metabolism  
0064   Dihydroxyacetone_kinases
0065   Entner-Doudoroff_Pathway
0066   Ethylmalonyl-CoA_pathway_of_C2_assimilation
0067   Glycolate,_glyoxylate_interconversions
0068   Glycolysis_and_Gluconeogenesis
0069   Glycolysis_and_Gluconeogenesis,_including_Archaeal_enzymes
0070   Glyoxylate_bypass
0071   Methylglyoxal_Metabolism
0072   Particulate_methane_monooxygenase_(pMMO)
0073   Pentose_phosphate_pathway
0074   Peripheral_Glucose_Catabolism_Pathways
0075   Pyruvate:ferredoxin_oxidoreductase
0076   Pyruvate_Alanine_Serine_Interconversions
0077   Pyruvate_metabolism_I:_anaplerotic_reactions,_PEP
0078   Pyruvate_metabolism_II:_acetyl-CoA,_acetogenesis_from_pyruvate
0079   Soluble_methane_monooxygenase_(sMMO)
0080   TCA_Cycle
0081 Di- and oligosaccharides Beta-Glucoside_Metabolism
0082   Fructooligosaccharides(FOS)_and_Raffinose_Utilization
0083   Lactose_and_Galactose_Uptake_and_Utilization
0084   Lactose_utilization
0085   Maltose_and_Maltodextrin_Utilization
0086   Melibiose_Utilization
0087   Sucrose_utilization
0088   Sucrose_utilization_Shewanella
0089   Trehalose_Biosynthesis
0090   Trehalose_Uptake_and_Utilization
0091   Unknown_oligosaccharide_utilization_Sde_1396
0092 Fermentation Acetoin,_butanediol_metabolism
0093   Acetone_Butanol_Ethanol_Synthesis
0094   Acetyl-CoA_fermentation_to_Butyrate
0095   Butanol_Biosynthesis
0096   Fermentations:_Lactate
0097   Fermentations:_Mixed_acid
0098 Glycoside hydrolases Predicted_carbohydrate_hydrolases
0099 Monosaccharides 2-Ketogluconate_Utilization
0100   D-Galacturonate_and_D-Glucuronate_Utilization
0101   D-Sorbitol(D-Glucitol)_and_L-Sorbose_Utilization
0102   D-Tagatose_and_Galactitol_Utilization
0103   D-allose_utilization
0104   D-galactarate,_D-glucarate_and_D-glycerate_catabolism
0105   D-galactonate_catabolism
0106   D-gluconate_and_ketogluconates_metabolism
0107   D-ribose_utilization
0108   Deoxyribose_and_Deoxynucleoside_Catabolism
0109   Fructose_utilization
0110   Hexose_Phosphate_Uptake_System
0111   L-Arabinose_utilization
0112   L-ascorbate_utilization_(and_related_gene_clusters)
0113   L-fucose_utilization
0114   L-fucose_utilization_temp
0115   L-rhamnose_utilization
0116   Mannose_Metabolism
0117   Xylose_utilization
0118 One-carbon Metabolism Formaldehyde_assimilation:_Ribulose_monophosphate_pathway
0119   Methanogenesis
0120   Methanogenesis_from_methylated_compounds
0121   One-carbon_metabolism_by_tetrahydropterines
0122   Serine-glyoxylate_cycle
0123 Organic acids 2-methylcitrate_to_2-methylaconitate_metabolism_cluster
0124   Alpha-acetolactate_operon
0125   Glycerate_metabolism
0126   Isobutyryl-CoA_to_Propionyl-CoA_Module
0127   Lactate_utilization
0128   Malonate_decarboxylase
0129   Methylcitrate_cycle
0130   Propionate-CoA_to_Succinate_Module
0131   Propionyl-CoA_to_Succinyl-CoA_Module
0132   Tricarballylate_Utilization
0133 Polysaccharides Alpha-Amylase_locus_in_Streptocococcus
0134   Cellulosome
0135   Glycogen_metabolism
0136   Unknown_carbohydrate_utilization_containing_Fructose-bisphosphate_aldolase
0137   Xyloglucan_Utilization
0138 Sugar alcohols Erythritol_utilization
0139   Ethanolamine_utilization
0140   Glycerol_and_Glycerol-3-phosphate_Uptake_and_Utilization
0141   Glycerol_fermenation_to_1,3-propanediol
0142   Inositol_catabolism
0143   Mannitol_Utilization
0144   Propanediol_utilization
0145 Unclassified carbohydrates Conserved_cluster_around_inner_membrane_protein_gene_yghQ,_probably_involved_in_polysaccharide_biosynthesis
0146   Lacto-N-Biose_I_and_Galacto-N-Biose_Metabolic_Pathway
0147   Sugar_utilization_in_Thermotogales
0148   Unknown_carbohydrate_utilization_(_cluster_Ydj_)
0149   Unknown_carbohydrate_utilization_(_cluster_Yeg_)
0150   Unknown_sugar_utilization_(cluster_yphABCDEFG)
0151   VC0266
0152   beta-glucuronide_utilization

13.4. Cell Wall and Capsule

si_# category subsystem
0162 Capsular and extracellular  
. polysacchrides Alginate_metabolism
0163   CMP-N-acetylneuraminate_Biosynthesis
0164   Capsular_Polysaccharide_(CPS)_of_Campylobacter
0165   Capsular_Polysaccharides_Biosynthesis_and_Assembly
0166   Capsular_heptose_biosynthesis
0167   Capsular_surface_virulence_antigen_loci
0168   Colanic_acid_biosynthesis
0169   Exopolysaccharide_Biosynthesis
0170   Extracellular_Polysaccharide_Biosynthesis_of_Streptococci
0171   Legionaminic_Acid_Biosynthesis
0172   O-Methyl_Phosphoramidate_Capsule_Modification_in_Campylobacter
0173   Phosphorylcholine_incorporation_in_LPS
0174   Polysaccharide_deacetylases
0175   Pseudaminic_Acid_Biosynthesis
0176   Rhamnose_containing_glycans
0177   Serotype_determining_Capsular_polysaccharide_biosynthesis_in_Staphylococcus
0178   Sialic_Acid_Metabolism
0179   Streptococcal_Hyaluronic_Acid_Capsule
0180   Vibrio_Polysaccharide_(VPS)_Biosynthesis
0181   Xanthan_Exopolysaccharide_Biosynthesis_and_Export
0182   YjbEFGH_Locus_Involved_in_Exopolysaccharide_Production
0183   dTDP-rhamnose_synthesis
0184 Cell wall of Mycobacteria mycolic_acid_synthesis
0185 Gram-Negative cell  
. wall components Core_Oligosaccharide_Glycosylation_in_Pseudomonas
0186   Inner_membrane_protein_YhjD_and_conserved_cluster_involved_in_LPS_biosynthesis
0187   KDO2-Lipid_A_biosynthesis
0188   LOS_core_oligosaccharide_biosynthesis
0189   Lipid_A-Ara4N_pathway_(_Polymyxin_resistance_)
0190   Lipid_A_modifications
0191   Lipopolysaccharide-related_cluster_in_Alphaproteobacteria
0192   Lipopolysaccharide_assembly
0193   Lipoprotein_sorting_system
0194   Major_Outer_Membrane_Proteins
0195   Outer_membrane
0196   Perosamine_Synthesis_Vibrio
0197   Vibrio_Core_Oligosaccharide_Biosynthesis
0198 Gram-Positive cell  
. wall components Anthrose_Biosynthesis
0199   D-Alanyl_Lipoteichoic_Acid_Biosynthesis
0200   Polyglycerolphosphate_lipoteichoic_acid_biosynthesis
0201   Sortase
0202   Teichoic_and_lipoteichoic_acids_biosynthesis
0203   Teichuronic_acid_biosynthesis
0204 Unclassified cell wall Murein_Hydrolases
. and capsule  
0205   Peptidoglycan_Biosynthesis
0206   Peptidoglycan_Crosslinking_of_Peptide_Stems
0207   Peptidoglycan_biosynthesis--gjo
0208   Recycling_of_Peptidoglycan_Amino_Acids
0209   Recycling_of_Peptidoglycan_Amino_Sugars
0210   UDP-N-acetylmuramate_from_Fructose-6-phosphate_Biosynthesis
0211   YjeE
0212   tRNA-dependent_amino_acid_transfers

13.5. Clustering-based subsystems

si_# category subsystem
0213 Biosynthesis of galacto- CBSS-258594.1.peg.3339
. glycans and related  
. lipopolysacharides  
0214   CBSS-376686.6.peg.291
0215 CRISPRs and associated CBSS-216592.1.peg.3534
. hypotheticals  
0216 Carbohydrates Beta-lactamase_cluster_in_Streptococcus
0217   Cluster_Ytf_and_putative_sugar_transporter
0218   Predicted_mycobacterial_monooxygenase
0219   Putative_sugar_ABC_transporter_(ytf_cluster)
0220 Carotenoid biosynthesis CBSS-320388.3.peg.3759
0221 Catabolism of an CBSS-262316.1.peg.2929
. unknown compound  
0222 Cell Division CBSS-393130.3.peg.794
0223   Cell_Division_Cluster
0224 Chemotaxis, response CBSS-323850.3.peg.3142
. regulators  
0225 Choline bitartrate CBSS-344610.3.peg.2335
. degradation, putative  
0226 Chromosome Replication SeqA_and_Co-occurring_Genes
0227 Clustering-based CBSS-262719.3.peg.410
. subsystems  
0228   CBSS-280355.3.peg.2835
0229   CBSS-292415.3.peg.2341
0230   Putative_diaminopropionate_ammonia-lyase_cluster
0231   Sporulation-related_Hypotheticals
0232 Cytochrome biogenesis CBSS-196164.1.peg.1690
0233   CBSS-196164.1.peg.461
0234   D-tyrosyl-tRNA(Tyr) deacylase (EC 3.1.-.-) cluster  CBSS-342610.3.peg.283
0235   DNA metabolism      CBSS-269801.1.peg.2186
0236   DNA polymerase III epsilon cluster  CBSS-342610.3.peg.1536
0237   Fatty acid metabolic cluster        CBSS-246196.1.peg.364
0238   Flagella protein?   CBSS-323098.3.peg.2823
0239   Hypothetical Related to Dihydroorate Dehydrogenase  Hypothetical_Related_to_Dihydroorotate_dehydrogenase
0240   Hypothetical associated with RecF   Hypothetical_Coupled_to_RecF
0241   Hypothetical in Lysine biosynthetic cluster CBSS-323850.3.peg.3269
0242   Hypothetical lipase related to Phosphatidate metabolism     CBSS-316407.3.peg.1371
0243   Hypothetical protein possible functionally linked with Alanyl-tRNA synthetase       CBSS-257314.1.peg.488
0244   Isoprenoid/cell wall biosynthesis: PREDICTED UNDECAPRENYL DIPHOSPHATE PHOSPHATASE   CBSS-83331.1.peg.3039
0245   Lysine Biosynthesis A_Glutathione-dependent_Thiol_Reductase_Associated_with_a_Step_in_Lysine_Biosynthesis
0246 Lysine, threonine, CBSS-84588.1.peg.1247
. methionine, and  
. cysteine  
0247   YeiH
0248   Membrane-bound hydrogenase  CBSS-69014.3.peg.2094
0249   Methylamine utilization     CBSS-265072.7.peg.546
0250   Molybdopterin oxidoreductase        CBSS-269799.3.peg.2220
0251   Monosaccharides     Unspecified_monosaccharide_transport_cluster
0252   Nucleotidyl-phosphate metabolic cluster     CBSS-222523.1.peg.1311
0253   Pigment biosynthesis        CBSS-176299.3.peg.235
0254   Probably GTP or GMP signaling related       CBSS-176299.4.peg.1292
0255   Probably Pyrimidine biosynthesis-related    CBSS-306254.1.peg.1508
0256   Probably Ybbk-related hypothetical membrane proteins        CBSS-316057.3.peg.659
0257   Probably organic hydroperoxide resistance related hypothetical protein      CBSS-269482.1.peg.1294
0258   Proteasome related clusters Proteasome_subunit_alpha_archaeal_cluster
0259   Protein export?     CBSS-393121.3.peg.2760
0260   Putative GGDEF domain protein related to agglutinin secretion       CBSS-323850.3.peg.3284
0261   Putative Isoquinoline 1-oxidoreductase subunit      CBSS-314267.3.peg.390
0262   Putative asociate of RNA polymerase sigma-54 factor rpoN    CBSS-316057.3.peg.1308
0263   Putrescine/GABA utilization cluster-temporal,to add to SSs  GABA_and_putrescine_metabolism_from_cluters
0264   Pyruvate kinase associated cluster  CBSS-288000.5.peg.1793
0265   Recombination related cluster       CBSS-198094.1.peg.4426
0266   Related to Menaquinone-cytochrome C reductase       CBSS-393130.3.peg.129
0267   Ribosomal Protein L28P ... A_Gram-positive_cluster_that_relates_ribosomal_protein_L28P_to_a_set_of_uncharacterized_proteins
0268   Ribosome-related cluster    A_Gammaproteobacteria_Cluster_Relating_to_Translation
0269   Sarcosine oxidase   CBSS-188.1.peg.6170
0270   Shiga toxin cluster CBSS-194948.1.peg.143
0271   Sulfatases and sulfatase modifying factor 1 (and a hypothetical)    Sulfatases_and_sulfatase_modifying_factor_1
0272   Three hypotheticals linked to lipoprotein biosynthesis      CBSS-188.1.peg.9880
0273   TldD cluster        CBSS-354.1.peg.2917
0274 Translation CBSS-243265.1.peg.198
0275   CBSS-326442.4.peg.1852
0276   Tricarboxylate transporter  CBSS-49338.1.peg.459
0277   Two related proteases       CBSS-257314.1.peg.676
0278   Type III secretion system, extended Type_III_secretion_systems,_extended
0279 Unclassified Bacterial_Cell_Division
0280   Bacterial_RNA-metabolizing_Zn-dependent_hydrolases
0281   CBSS-138119.3.peg.2719
0282   CBSS-159087.4.peg.2189
0283   CBSS-160492.1.peg.550
0284   CBSS-176279.3.peg.1262
0285   CBSS-176279.3.peg.868
0286   CBSS-176280.1.peg.1561
0287   CBSS-196620.1.peg.2477
0288   CBSS-214092.1.peg.3450
0289   CBSS-224911.1.peg.435
0290   CBSS-228410.1.peg.134
0291   CBSS-235.1.peg.567
0292   CBSS-243277.1.peg.4359
0293   CBSS-251221.1.peg.1863
0294   CBSS-257314.1.peg.752
0295   CBSS-261594.1.peg.2640
0296   CBSS-266117.6.peg.2476
0297   CBSS-269801.1.peg.1715
0298   CBSS-269801.1.peg.1725
0299   CBSS-281090.3.peg.464
0300   CBSS-288681.3.peg.1039
0301   CBSS-290633.1.peg.1906
0302   CBSS-291331.3.peg.3674
0303   CBSS-296591.1.peg.2330
0304   CBSS-312309.3.peg.1965
0305   CBSS-314269.3.peg.1840
0306   CBSS-316057.3.peg.3521
0307   CBSS-316057.3.peg.563
0308   CBSS-316273.3.peg.227
0309   CBSS-316273.3.peg.2378
0310   CBSS-316273.3.peg.2709
0311   CBSS-316273.3.peg.448
0312   CBSS-316273.3.peg.922
0313   CBSS-316279.3.peg.746
0314   CBSS-316407.3.peg.2816
0315   CBSS-320372.3.peg.6046
0316   CBSS-323097.3.peg.2594
0317   CBSS-342610.3.peg.1794
0318   CBSS-345072.3.peg.1318
0319   CBSS-350688.3.peg.1509
0320   CBSS-370552.3.peg.1240
0321   CBSS-393121.3.peg.1913
0322   CBSS-393124.3.peg.2657
0323   CBSS-393131.3.peg.612
0324   CBSS-393133.3.peg.2787
0325   CBSS-562.2.peg.5158_SK3_including
0326   CBSS-56780.10.peg.1536
0327   CBSS-630.2.peg.3360
0328   CBSS-83332.1.peg.3803
0329   CBSS-83333.1.peg.946
0330   CBSS-87626.3.peg.3639
0331   Cell_division-ribosomal_stress_proteins_cluster
0332   Conserved_cluster_around_acetyltransferase_YpeA_in_Enterobacteria
0333   Conserved_cluster_in_Enterobacteriaceae_downstream_from_YqjA,_a_DedA_family_protein
0334   Conserved_gene_cluster_associated_with_Met-tRNA_formyltransferase
0335   EC49-61
0336   EC699-706
0337   KH_domain_RNA_binding_protein_YlqC
0338   LMPTP_YfkJ_cluster
0339   LMPTP_YwlE_cluster
0340   NusA-TFII_Cluster
0341   PA0057_cluster
0342   Putative_hemin_transporter
0343   Putative_sulfate_assimilation_cluster
0344   Spore_Coat
0345   Staphylococcus_aureus_hypothetical_repetitive_gene_loci
0346   USS-DB-1
0347   USS-DB-2
0348   USS-DB-4
0349   USS-DB-6
0350   USS-DB-7
0351   Yfa_cluster
0352   Urate degradation   CBSS-205922.3.peg.1809
0353   alpha-proteobacterial cluster of hypotheticals      CBSS-52598.3.peg.2843
0354   proteosome related  Cluster-based_Subsystem_Grouping_Hypotheticals_-_perhaps_Proteosome_Related
0355   recX and regulatory cluster CBSS-261594.1.peg.788
0356   tRNA sulfuration    CBSS-89187.3.peg.2957

13.6. Cofactors, Vitamins, Prosthetic Groups, Pigments

si_# category subsystem
0357 Biotin Biotin_biosynthesis
0358 Coenzyme A Coenzyme_A_Biosynthesis
0359 Coenzyme B Coenzyme_B_synthesis
0360 Coenzyme F420 Coenzyme_F420_synthesis
0361 Coenzyme M coenzyme_M_biosynthesis
0362 Folate and pterines 5-FCL-like_protein
0363   Folate_Biosynthesis
0364   Methanopterin_biosynthesis2
0365   Molybdenum_cofactor_biosynthesis
0366   Pterin_biosynthesis
0367   Pterin_carbinolamine_dehydratase
0368   Pterin_metabolism
0369   Pterin_metabolism_3
0370   methanopterin_biosynthesis
0371   p-Aminobenzoyl-Glutamate_Utilization
0372 Lipoic acid Lipoic_acid_metabolism
0373 NAD and NADP NAD_and_NADP_cofactor_biosynthesis_global
0374   NAD_consumption
0375   NAD_regulation
0376 Pyridoxine Pyridoxin(Vitamin_B6)_Degradation_Pathway
0377   Pyridoxin_(Vitamin_B6)_Biosynthesis
0378 Quinone cofactors Coenzyme_PQQ_synthesis
0379   Menaquinone_Biosynthesis_via_Futalosine_--_gjo
0380   Menaquinone_and_Phylloquinone_Biosynthesis
0381   Plastoquinone_Biosynthesis
0382   Pyrroloquinoline_Quinone_biosynthesis
0383   Tocopherol_Biosynthesis
0384   Ubiquinone_Biosynthesis
0385 Riboflavin, FMN, FAD Flavodoxin
0386   Riboflavin,_FMN_and_FAD_metabolism
0387   riboflavin_to_FAD
0388 Tetrapyrroles Bilin_Biosynthesis
0389   Chlorophyll_Biosynthesis
0390   Chlorophyll_Degradation
0391   Cobalamin_synthesis
0392   Coenzyme_B12_biosynthesis
0393   Heme_and_Siroheme_Biosynthesis
0394   Heme_biosynthesis_orphans
0395 Unclassified Molybdopterin_cytosine_dinucleotide
0396   Thiamin_biosynthesis

13.11. Membrane Transport

si_# category subsystem
0488 ABC transporters ABC_transporter_alkylphosphonate_(TC_3.A.1.9.1)
0489   ABC_transporter_branched-chain_amino_acid_(TC_3.A.1.4.1)
0490   ABC_transporter_dipeptide_(TC_3.A.1.5.2)
0491   ABC_transporter_of_unknown_substrate_X
0492   ABC_transporter_oligopeptide_(TC_3.A.1.5.1)
0493   ABC_transporter_peptide_(TC_3.A.1.5.5)
0494   ABC_transporter_tungstate_(TC_3.A.1.6.2)
0495   ATP-dependent_efflux_pump_transporter_Ybh
0496   Periplasmic-Binding-Protein-Dependent_Transport_System_for_α-Glucosides
0497 Protein and nucleoprotein Dot-Icm_type_IV_secretion_system
. secretion system, Type IV  
0498   Mannose-sensitive_hemagglutinin_type_4_pilus
0499   Toxin_co-regulated_pilus
0500   Type_4_conjugative_transfer_system,_IncI1_type
0501   Type_IV_pilus
0502   pVir_Plasmid_of_Campylobacter
0503 Protein secretion system, General_Secretion_Pathway
. Type II  
0504   Widespread_colonization_island
0505 Protein secretion system, Type_III_secretion_system
. Type III  
0506   Type_III_secretion_system_orphans
0507 Protein secretion system, Type_VI_secretion_systems
. Type VI  
0508 Protein secretion system, Colonization_factor_antigen_I_fimbriae
. Type VII (Chaperone/Usher  
. pathway, CU)  
0509   The_fimbrial_Sfm_cluster
0510   The_fimbrial_Stf_cluster
0511   The_usher_protein_HtrE_fimbrial_cluster
0512 Protein secretion system, Curli_production
. Type VIII (Extracellular  
. nucleation/precipitation  
. pathway, ENP)  
0513 Protein translocation ESAT-6_proteins_secretion_system_in_Actinobacteria
. across cytoplasmic  
. membrane  
0514   ESAT-6_proteins_secretion_system_in_Firmicutes
0515   HtrA_and_Sec_secretion
0516   SecY2-SecA2_Specialized_Transport_System
0517   Twin-arginine_translocation_system
0518 Sugar Phosphotransferase Fructose_and_Mannose_Inducible_PTS
. Systems, PTS  
0519   Galactose-inducible_PTS
0520   Sucrose-specific_PTS
0521 Unclassified Agrobacterium_opine_transport
0522   Choline_Transport
0523   Citrate_Utilization_System_(CitAB,_CitH,_and_tctABC)
0524   ECF_class_transporters
0525   Phosphoglycerate_transport_system
0526   Ton_and_Tol_transport_systems
0527   Transport_of_Manganese
0528   Transport_of_Molybdenum
0529   Transport_of_Nickel_and_Cobalt
0530   Transport_of_Zinc
0531 Uni- Sym- and Antiporters Na(+)_H(+)_antiporter
0532   Proton-dependent_Peptide_Transporters
0533   Sodium_Hydrogen_Antiporter

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

13.17. 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

13.19. 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

13.21. Protein Metabolism

si_# category subsystem
0656 Protein biosynthesis Nucleolar_protein_complex
0657   Programmed_frameshift
0658   Pyrrolysine
0659   Ribosomal_protein_paralogs
0660   Ribosome_LSU_bacterial
0661   Ribosome_LSU_eukaryotic_and_archaeal
0662   Ribosome_SSU_bacterial
0663   Ribosome_SSU_eukaryotic_and_archaeal
0664   Ribosome_activity_modulation
0665   Ribosome_biogenesis_bacterial
0666   Trans-translation_by_stalled_ribosomes
0667   Translation_elongation_factor_G_family
0668   Translation_elongation_factors_bacterial
0669   Translation_elongation_factors_eukaryotic_and_archaeal
0670   Translation_initiation_factors_bacterial
0671   Translation_initiation_factors_eukaryotic_and_archaeal
0672   Translation_termination_factors_bacterial
0673   Universal_GTPases
0674   tRNA_aminoacylation,_Ala
0675   tRNA_aminoacylation,_Arg
0676   tRNA_aminoacylation,_Asp_and_Asn
0677   tRNA_aminoacylation,_Cys
0678   tRNA_aminoacylation,_Glu_and_Gln
0679   tRNA_aminoacylation,_Gly
0680   tRNA_aminoacylation,_His
0681   tRNA_aminoacylation,_Ile
0682   tRNA_aminoacylation,_Leu
0683   tRNA_aminoacylation,_Lys
0684   tRNA_aminoacylation,_Met
0685   tRNA_aminoacylation,_Phe
0686   tRNA_aminoacylation,_Pro
0687   tRNA_aminoacylation,_Pyr
0688   tRNA_aminoacylation,_Ser
0689   tRNA_aminoacylation,_Thr
0690   tRNA_aminoacylation,_Trp
0691   tRNA_aminoacylation,_Tyr
0692   tRNA_aminoacylation,_Val
0693 Protein degradation Aminopeptidases_(EC_3.4.11.-)
0694   Dipeptidases_(EC_3.4.13.-)
0695   Metallocarboxypeptidases_(EC_3.4.17.-)
0696   Metalloendopeptidases_(EC_3.4.24.-)
0697   Omega_peptidases_(EC_3.4.19.-)
0698   Proteasome_archaeal
0699   Proteasome_bacterial
0700   Protein_degradation
0701   Proteolysis_in_bacteria,_ATP-dependent
0702   Putative_TldE-TldD_proteolytic_complex
0703   Serine_endopeptidase_(EC_3.4.21.-)
0704 Protein folding GroEL_GroES
0705   Peptidyl-prolyl_cis-trans_isomerase
0706   Periplasmic_disulfide_interchange
0707   Protein_chaperones
0708   Thermosome,_archaeal
0709 Protein processing and Inteins
. modification  
0710   Lipoprotein_Biosynthesis
0711   N-linked_Glycosylation_in_Bacteria
0712   Peptide_methionine_sulfoxide_reductase
0713   Protein_Acetylation_and_Deacetylation_in_Bacteria
0714   Ribosomal_protein_S12p_Asp_methylthiotransferase
0715   Ribosomal_protein_S5p_acylation
0716   Signal_peptidase
0717   Ubiquitin-like_archaeal_modifier_proteins_(SAMPs)
0718 Secretion Protein_secretion_by_ABC-type_exporters
0719 Selenoproteins Glycine_reductase,_sarcosine_reductase_and_betaine_reductase
0720   Selenocysteine_metabolism
0721   Selenoprotein_O

13.23. Regulation and Cell signaling

si_# category subsystem
0753 Programmed Cell Death and A_toxin-antitoxin_module_cotranscribed_with_DinB
. Toxin-antitoxin Systems  
0754   Bacterial_Caspases
0755   Fratricide_in_Streptococcus
0756   MazEF_toxin-antitoxing_(programmed_cell_death)_system
0757   Murein_hydrolase_regulation_and_cell_death
0758   Phd-Doc,_YdcE-YdcD_toxin-antitoxin_(programmed_cell_death)_systems
0759   Toxin-antitoxin_replicon_stabilization_systems
0760   Toxin-antitoxin_systems_(other_than_RelBE_and_MazEF)
0761 Quorum sensing and Autoinducer_2_(AI-2)_transport_and_processing_(lsrACDBFGE_operon)
. biofilm formation  
0762   Biofilm_Adhesin_Biosynthesis
0763   Biofilm_formation_in_Staphylococcus
0764   Quorum-sensing_in_Vibrio
0765   Quorum_sensing_in_Yersinia
0766   Quorum_sensing_regulation_in_Pseudomonas
0767   Symbiotic_colonization_and_sigma-dependent_biofilm_formation_gene_cluster
0768 Regulation of virulence A_conserved_operon_linked_to_TyrR_and_possibly_involved_in_virulence
0769   SpeB-SpeF_extended_regulon
0770   Streptococcal_Mga_Regulon
0771   Streptococcus_pyogenes_virulence_regulators
0772   Two-component_Response_Regulator_of_Virulence_ResDE
0773   VieSAB_signal_transduction_system_of_Vibrio
0774 Unclassified Cell_envelope-associated_LytR-CpsA-Psr_transcriptional_attenuators
0775   CytR_regulation
0776   DNA-binding_regulatory_proteins,_strays
0777   Global_Two-component_Regulator_PrrBA_in_Proteobacteria
0778   HPr_catabolite_repression_system
0779   Orphan_regulatory_proteins
0780   Oxygen_and_light_sensor_PpaA-PpsR
0781   Pseudomonas_quinolone_signal_PQS
0782   Rcs_phosphorelay_signal_transduction_pathway
0783   Sex_pheromones_in_Enterococcus_faecalis_and_other_Firmicutes
0784   Stringent_Response,_(p)ppGpp_metabolism
0785   The_Chv_regulatory_system_of_Alphaproteobacteria
0786   Trans-envelope_signaling_system_VreARI_in_Pseudomonas
0787   Two-component_regulatory_systems_in_Campylobacter
0788   WhiB_and_WhiB-type_regulatory_proteins_
0789   Zinc_regulated_enzymes
0790   cAMP_signaling_in_bacteria

13.24. Respiration

si_# category subsystem
0791 ATP synthases F0F1-type_ATP_synthase
0792   V-Type_ATP_synthase
0793 Electron accepting reactions Anaerobic_respiratory_reductases
0794   Terminal_AA3-600_quinol_oxidase
0795   Terminal_cytochrome_C_oxidases
0796   Terminal_cytochrome_O_ubiquinol_oxidase
0797   Terminal_cytochrome_d_ubiquinol_oxidases
0798   Terminal_cytochrome_oxidases
0799   Tetrathionate_respiration
0800   Ubiquinone_Menaquinone-cytochrome_c_reductase_complexes
0801   trimethylamine_N-oxide_(TMAO)_reductase
0802 Electron donating reactions CO_Dehydrogenase
0803   Coenzyme_F420-H2_dehydrogenase_(methanophenazine)
0804   Coenzyme_F420_hydrogenase
0805   Energy-conserving_hydrogenase_(ferredoxin)
0806   Formate_dehydrogenase
0807   H2:CoM-S-S-HTP_oxidoreductase
0808   Hydrogenases
0809   Methanophenazine_hydrogenase
0810   Na(+)-translocating_NADH-quinone_oxidoreductase_and_rnf-like_group_of_electron_transport_complexes
0811   NiFe_hydrogenase_maturation
0812   Respiratory_Complex_I
0813   Respiratory_dehydrogenases_1
0814   Succinate_dehydrogenase
0815 Sodium Ion-Coupled Na+_translocating_decarboxylases_and_related_biotin-dependent_enzymes
. Energetics  
0816 Unclassified Biogenesis_of_c-type_cytochromes
0817   Biogenesis_of_cbb3-type_cytochrome_c_oxidases
0818   Biogenesis_of_cytochrome_c_oxidases
0819   Carbon_monoxide_dehydrogenase_maturation_factors
0820   Carbon_monoxide_induced_hydrogenase
0821   Cytochrome_B6-F_complex
0822   Flavocytochrome_C
0823   Formate_hydrogenase
0824   Quinone_oxidoreductase_family
0825   Reductive_Dechlorination
0826   Soluble_cytochromes_and_functionally_related_electron_carriers

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

si_# category subsystem
0843 Acid stress Acid_resistance_mechanisms
0844   Glutamate_transporter_involved_in_acid_tolerance_in_Streptococcus
0845 Cold shock Cold_shock,_CspA_family_of_proteins
0846 Dessication stress O-antigen_capsule_important_for_environmental_persistence
0847 Detoxification D-tyrosyl-tRNA(Tyr)_deacylase
0848   Glutathione-dependent_pathway_of_formaldehyde_detoxification
0849   Tellurite_resistance:_Chromosomal_determinants
0850   Uptake_of_selenate_and_selenite
0851 Heat shock Heat_shock_dnaK_gene_cluster_extended
0852 Osmotic stress Betaine_biosynthesis_from_glycine
0853   Choline_and_Betaine_Uptake_and_Betaine_Biosynthesis
0854   Ectoine_biosynthesis_and_regulation
0855   Osmoprotectant_ABC_transporter_YehZYXW_of_Enterobacteriales
0856   Osmoregulation
0857   Synthesis_of_osmoregulated_periplasmic_glucans
0858   Glutaredoxins
0859   Glutathione:_Biosynthesis_and_gamma-glutamyl_cycle
0860   Glutathione:_Non-redox_reactions
0861   Glutathione:_Redox_cycle
0862   Glutathione_analogs:_mycothiol
0863   Glutathionylspermidine_and_Trypanothione
0864   Oxidative_stress
0865   Protection_from_Reactive_Oxygen_Species
0866   Redox-dependent_regulation_of_nucleus_processes
0867   Regulation_of_Oxidative_Stress_Response
0868   Rubrerythrin
0869 Periplasmic Stress Periplasmic_Acid_Stress_Response_in_Enterobacteria
0870   Periplasmic_Stress_Response
0871 Unclassified Bacterial_hemoglobins
0872   Carbon_Starvation
0873   Commensurate_regulon_activation
0874   Dimethylarginine_metabolism
0875   Flavohaemoglobin
0876   Hfl_operon
0877   Phage_shock_protein_(psp)_operon
0878   SigmaB_stress_responce_regulation
0879   Sugar-phosphate_stress_regulation
0880   Universal_stress_protein_family

13.28. Virulence, Disease, and Defense

si_# category subsystem
0894 Adhesion Type_1_pili_(mannose-sensitive_fimbriae)
0895 Fimbriae of the Chaperone α-Fimbriae
. /Usher Assembly Pathway  
0896   α-related_Fimbriae_in_Yersinia
0897   β-Fimbriae
0898   κ-Fimbriae
0899   σ-Fimbriae
0900 Quorum sensing and Acyl_Homoserine_Lactone_(AHL)_Autoinducer_Quorum_Sensing_
. biofilm formation  
0901 Resistance to antibiotics BlaR1_Family_Regulatory_Sensor-transducer_Disambiguation
. and toxic compounds  
0902   Erythromycin_resistance
0903   Polymyxin_Synthetase_Gene_Cluster_in_Bacillus
0904 Toxins and superantigens Diphtheria_toxin
0905   Streptococcus_agalactiae_hemolysin_operon
0906 Type III, Type IV, Type Type_4_secretion_and_conjugative_transfer
. VI, ESAT secretion systems  
0907 Unclassified virulence Streptococcus_agalactiae_virulome
0908 Adhesion Accessory_colonization_factor
0909   Adhesins_in_Staphylococcus
0910   Adhesion_of_Campylobacter
0911   Decorin_binding_proteins_of_Borrelia
0912   Mediator_of_hyperadherence_YidE_in_Enterobacteria_and_its_conserved_region
0913   Streptococcus_pyogenes_recombinatorial_zone
0914 Bacteriocins, ribosomally Bacitracin_Stress_Response
. synthesized antibacterial  
. peptides  
0915   Bacteriocin-like_peptides_Blp
0916   Marinocine,_a_broad-spectrum_antibacterial_protein
0917   Tolerance_to_colicin_E2
0918 Detection MLST
0919 Invasion and Cytolysin_and_Lipase_operon_in_Vibrio
. intracellular resistance  
0920   Gram-Positive_Extracellular_Nucleases
0921   Listeria_surface_proteins:_Internalin-like_proteins
0922   Listeria_surface_proteins:_LPXTG_motif
0923   Salmonella_invasion_locus
0924 Resistance to antibiotics Adaptation_to_d-cysteine
. and toxic compounds  
0925   Aminoglycoside_adenylyltransferases
0926   Arsenic_resistance
0927   Beta-lactamase
0928   Cadmium_resistance
0929   Cobalt-zinc-cadmium_resistance
0930   Copper_homeostasis
0931   Fosfomycin_resistance
0932   Lysozyme_inhibitors
0933   Mercuric_reductase
0934   Mercury_resistance_operon
0935   Methicillin_resistance_in_Staphylococci
0936   MexA-MexB-OprM_Multidrug_Efflux_System
0937   MexC-MexD-OprJ_Multidrug_Efflux_System
0938   MexE-MexF-OprN_Multidrug_Efflux_System
0939   Multidrug_Resistance_Efflux_Pumps
0940   Multidrug_Resistance_Operon_mdtRP_of_Bacillus
0941   Multidrug_efflux_pump_in_Campylobacter_jejuni_(CmeABC_operon)
0942   Multiple_Antibiotic_Resistance_MAR_locus
0943   Resistance_to_Vancomycin
0944   Resistance_to_chromium_compounds
0945   Resistance_to_fluoroquinolones
0946   Streptococcus_pneumoniae_Vancomycin_Tolerance_Locus
0947   Streptothricin_resistance
0948   Teicoplanin-resistance_in_Staphylococcus
0949   The_mdtABCD_multidrug_resistance_cluster
0950   Zinc_resistance
0951 Toxins and superantigens Cholera_toxin
0952   Cytolethal_distending_toxin_of_Campylobacter_jejuni
0953   Cytolethal_distending_toxins
0954   Pertussis_toxin
0955   Prophage-encoded_Exotoxins
0956   SLO-NADGH_Locus
0957   Staphylococcus_Two-component_and_Pore-forming_Cytolysins
0958   Streptolysin_S_Biosynthesis_and_Transport
0959 Unclassified Bacterial_cyanide_production_and_tolerance_mechanisms
0960   C_jejuni_colonization_of_chick_caeca
0961   Streptococcus_pyogenes_Virulome

13.29. Ribosome

si_# category subsystem
0962 Ribosome Ribosome

13.30. 0963 No Function Match