16S_rRNA_modification_within_P_site_of_ribosome	1
2-phosphoglycolate_salvage	-1
4-Hydroxyphenylacetic_acid_catabolic_pathway	-1
5-FCL-like_protein	5
ABC_transporter_[iron.B12.siderophore.hemin]	1
ABC_transporter_dipeptide_(TC_3.A.1.5.2)	2
ABC_transporter_oligopeptide_(TC_3.A.1.5.1)	3
ATP-dependent_RNA_helicases,_bacterial	1
A_Gammaproteobacteria_Cluster_Relating_to_Translation	9.x
A_Glutathione-dependent_Thiol_Reductase_Associated_with_a_Step_in_Lysine_Biosynthesis	-1
A_Hypothetical_Protein_Related_to_Proline_Metabolism	1
A_Hypothetical_that_Clusters_with_PEP_Synthase	1
Acetoin,_butanediol_metabolism	2.2
Acetolactate_synthase_subunits	1
Acetyl-CoA_fermentation_to_Butyrate	B
Acyl-CoA_thioesterase_II	1
Adenosyl_nucleosidases	1
Alanine_biosynthesis	C
Alkanesulfonates_Utilization	26
Alkylphosphonate_utilization	-1
Allantoin_Utilization	X
Alpha-Amylase_locus_in_Streptocococcus	3
Alpha-acetolactate_operon	-1
Aminopeptidases_(EC_3.4.11.-)	1
Ammonia_assimilation	4
Anaerobic_respiratory_reductases	3.92
Arginine_Biosynthesis_--_gjo	1.1
Arginine_Biosynthesis_extended	1.1
Arginine_Deiminase_Pathway	1.x
Aromatic_Amin_Catabolism	6
Aromatic_amino_acid_degradation	-1
Aromatic_dioxygenase_mess	1
Arsenic_resistance	1
Bacillus_subtilis_scratch_-_gjo	1
Bacterial_Cell_Division	10
Bacterial_Chemotaxis	9
Bacterial_Cytoskeleton	1.123
Bacterial_hemoglobins	1.2
Bacterial_signal_recognition_particle_(SRP)	1
Benzoate_degradation	3
Beta-Glucoside_Metabolism	-1
Beta-lactamase	1
Bilin_Biosynthesis	-1
Biofilm_formation_in_Staphylococcus	-1
Biogenesis_of_c-type_cytochromes	2
Biogenesis_of_cytochrome_c_oxidases	3
Biotin_biosynthesis	2X
Biotin_biosynthesis_Experimental	2
Branched-Chain_Amino_Acid_Biosynthesis	7
Broadly_distributed_proteins_not_in_subsystems	1
Butanol_Biosynthesis	2
Butyrate_metabolism_cluster	1
CBSS-1352.1.peg.856	5
CBSS-138119.3.peg.2719	9
CBSS-176279.3.peg.868	1.x
CBSS-176280.1.peg.1561	-1
CBSS-176299.4.peg.1292	3
CBSS-196164.1.peg.1690	1
CBSS-196164.1.peg.461	2
CBSS-216591.1.peg.168	1
CBSS-216600.3.peg.802	1
CBSS-224308.1.peg.3555	-1
CBSS-228410.1.peg.134	2
CBSS-243265.1.peg.198	-1
CBSS-246196.1.peg.364	1
CBSS-257314.1.peg.752	-1
CBSS-266117.6.peg.1260	2
CBSS-269482.1.peg.1294	2
CBSS-272943.3.peg.1367	1
CBSS-290633.1.peg.1906	-1
CBSS-291331.3.peg.3674	-1
CBSS-292415.3.peg.2341	-1
CBSS-296591.1.peg.2330	-1
CBSS-312309.3.peg.1965	2.x
CBSS-314276.3.peg.1499	1
CBSS-315749.4.peg.3658	-1
CBSS-316057.3.peg.1308	-1
CBSS-316057.3.peg.3521	1
CBSS-316057.3.peg.563	9
CBSS-316273.3.peg.2378	-1
CBSS-320388.3.peg.3759	-1
CBSS-323850.3.peg.3269	-1
CBSS-326442.4.peg.1852	-1
CBSS-331978.3.peg.2915	1
CBSS-342610.3.peg.1536	2
CBSS-342610.3.peg.1794	-1
CBSS-342610.3.peg.283	1
CBSS-349102.4.peg.3442	1
CBSS-349161.4.peg.2417	1.x
CBSS-36873.1.peg.4752	-1
CBSS-393121.3.peg.1913	-1
CBSS-393124.3.peg.2657	-1
CBSS-393130.3.peg.794	-1
CBSS-393133.3.peg.2787	-1
CBSS-410289.13.peg.3174	-1
CBSS-479431.5.peg.3955	1
CBSS-56780.10.peg.1536	1
CBSS-83333.1.peg.946	-1
CBSS-84588.1.peg.1247	1
CBSS-87626.3.peg.3639	-1
CBSS-89187.3.peg.2957	-1
CO2_uptake,_carboxysome	6
CRISPRs	1
CTP_synthase_(EC_6.3.4.2)_cluster	9
Calvin-Benson_cycle	-1
Campylobacter_Iron_Metabolism	-1
Capsular_Polysaccharides_Biosynthesis_and_Assembly	-1
Capsular_heptose_biosynthesis	-1
Carbon_Starvation	1.1
Cardiolipin_synthesis	1
Catechol_branch_of_beta-ketoadipate_pathway	3.x
Cell_division-ribosomal_stress_proteins_cluster	1
Cell_division_cluster_containing_FtsZ_and_FtsW	1.x
Cell_envelope-associated_LytR-CpsA-Psr_transcriptional_attenuators	1
Chloroaromatic_degradation_pathway	-1
Chlorobenzoate_degradation	-1
Choline_and_Betaine_Uptake_and_Betaine_Biosynthesis	1.3
Choline_uptake_and_conversion_to_betaine_clusters	9.x
Chorismate:_Intermediate_for_synthesis_of_Tryptophan,_PAPA_antibiotics,_PABA,_3-hydroxyanthranilate_and_more.	missing
Cluster-based_Subsystem_Grouping_Hypotheticals_-_perhaps_Proteosome_Related	5.x
Cluster_containing_Alanyl-tRNA_synthetase	1.x
Cobalamin_synthesis	-1
Cobalt-zinc-cadmium_resistance	7.69
Coenzyme_A_Biosynthesis	A.2111
Coenzyme_A_Biosynthesis_cluster	1.x
Coenzyme_M_biosynthesis_--_gjo	-1
Cold_shock,_CspA_family_of_proteins	1
Common_Pathway_For_Synthesis_of_Aromatic_Compounds_(DAHP_synthase_to_chorismate)	missing
Conserved_gene_cluster_possibly_involved_in_RNA_metabolism	-1
Control_of_cell_elongation_-_division_cycle_in_Bacilli	-1
Copper_Transport_System	1.0x
Copper_homeostasis	9.xx
Creatine_and_Creatinine_Degradation	4.x
Cyanate_hydrolysis	-1
Cysteine_Biosynthesis	2.17
D-Tagatose_and_Galactitol_Utilization	-1
D-galactarate,_D-glucarate_and_D-glycerate_catabolism	-1
D-galactarate,_D-glucarate_and_D-glycerate_catabolism_-_gjo	-1
D-ribose_utilization	B.1
D-tyrosyl-tRNA(Tyr)_deacylase	1
DNA_Repair_Base_Excision	4
DNA_gyrase_subunits	2
DNA_ligases	1
DNA_processing_cluster	9
DNA_repair,_UvrABC_system	1
DNA_repair,_bacterial	1
DNA_repair,_bacterial_DinG_and_relatives	1.0100
DNA_repair,_bacterial_RecBCD_pathway	1
DNA_repair,_bacterial_RecFOR_pathway	1
DNA_repair,_bacterial_UmuCD_system	-1
DNA_repair,_bacterial_UvrD_and_related_helicases	1
DNA_repair_system_including_RecA,_MutS_and_a_hypothetical_protein	2.x
DNA_replication,_archaeal	-1
DNA_replication_cluster_1	2
DNA_structural_proteins,_bacterial	-1
DNA_topoisomerases,_Type_I,_ATP-independent	1
DNA_topoisomerases,_Type_II,_ATP-dependent	1.000
De_Novo_Purine_Biosynthesis	1
De_Novo_Pyrimidine_Synthesis	1
DedA_family_of_inner_membrane_proteins	1
Dehydrogenase_complexes	1.3002
Deoxyribose_and_Deoxynucleoside_Catabolism	3.0
Di-Inositol-Phosphate_biosynthesis	-1
Dioxygenases_(EC_1.13.11.-)	1
Dioxygenases_(EC_1.14.12.-)	1
Dissimilatory_nitrite_reductase	-1
ECF_class_transporters	8
Encapsulating_protein_for_DyP-type_peroxidase_and_ferritin-like_protein_oligomers	1
Entner-Doudoroff_Pathway	-1
Ethanolamine_utilization	-1
Ethylmalonyl-CoA_pathway_of_C2_assimilation,_GJO	-1
Fatty_Acid_Biosynthesis_FASII	D
Fatty_acid_metabolism_cluster	6
Fermentations:_Lactate	1.10
Fermentations:_Mixed_acid	-1
Flagellum	-1
Flagellum_in_Campylobacter	-1
Flavohaemoglobin	1
Folate_Biosynthesis	111
Folate_biosynthesis_cluster	2.x
Formate_hydrogenase	7
Fructooligosaccharides(FOS)_and_Raffinose_Utilization	-1
Fructose_utilization	1
G3E_family_of_P-loop_GTPases_(metallocenter_biosynthesis)	1
Gentisate_degradation	3
Glutamate_and_Aspartate_uptake_in_Bacteria	5.0
Glutamate_dehydrogenases	1
Glutamine,_Glutamate,_Aspartate_and_Asparagine_Biosynthesis	1.1234
Glutamine_synthetases	6
Glutaredoxins	3
Glutathione:_Biosynthesis_and_gamma-glutamyl_cycle	-1
Glutathione:_Non-redox_reactions	9
Glutathione:_Redox_cycle	?
Glutathione_analogs:_mycothiol	1
Glutathionylspermidine_and_Trypanothione	9
Glycerate_metabolism	1
Glycerol_and_Glycerol-3-phosphate_Uptake_and_Utilization	7.0
Glycerolipid_and_Glycerophospholipid_Metabolism_in_Bacteria	1.x
Glycine_Biosynthesis	1.0
Glycine_and_Serine_Utilization	1.13
Glycine_cleavage_system	1
Glycine_reductase,_sarcosine_reductase_and_betaine_reductase	-1
Glycolysis_and_Gluconeogenesis	1.2112
Glycolysis_and_Gluconeogenesis,_including_Archaeal_enzymes	-1
Glycyl-tRNA_synthetase_containing_cluster	9.x
Glyoxylate_bypass	1
Glyoxylate_bypass_cluster	9
GroEL_GroES	1
Heat_shock_dnaK_gene_cluster_extended	2.2
Heme,_hemin_uptake_and_utilization_systems_in_GramNegatives	-1
Heme,_hemin_uptake_and_utilization_systems_in_GramPositives	7
Heme_and_Siroheme_Biosynthesis	5.1919
Hfl_operon	1.010
High_affinity_phosphate_transporter_and_control_of_PHO_regulon	1
Histidine_Biosynthesis	missing
Homogentisate_pathway_of_aromatic_compound_degradation	-1
Housecleaning_nucleoside_triphosphate_pyrophosphatases	1
Hydantoin_metabolism	6
Hydroxyaromatic_decarboxylase_family	1
Hypothetical_Coupled_to_RecF	1
Inteins	-1
Iron-sulfur_cluster_assembly	1
Isoprenoid_Biosynthesis	2.9
KH_domain_RNA_binding_protein_YlqC	-1
Ketoisovalerate_oxidoreductase	-1
L-rhamnose_utilization	-1
LMPTP_YfkJ_cluster	93
LOS_core_oligosaccharide_biosynthesis	-1
LSU_ribosomal_proteins_cluster	2
Lactate_utilization	1
Lacto-N-Biose_I_and_Galacto-N-Biose_Metabolic_Pathway	-1
Lactose_and_Galactose_Uptake_and_Utilization	4.x
Lanthionine_Synthetases	-1
Leucine_Biosynthesis	1.0
Lipid-linked_oligosaccharide_synthesis_related_cluster	1.x
Lipoic_acid_metabolism	7.0
Lipoic_acid_synthesis_cluster	2
Lipoprotein_Biosynthesis	1
LysR-family_proteins_in_Escherichia_coli	1
LysR-family_proteins_in_Salmonella_enterica_Typhimurium	1
Lysine_Biosynthesis_DAP_Pathway,_GJO_scratch	0.001
Lysine_fermentation	-1
Magnesium_transport	1
Mannitol_Utilization	-1
Mannose_Metabolism	1.1x1
Menaquinone_Biosynthesis_via_Futalosine	-1
Menaquinone_and_Phylloquinone_Biosynthesis	2.x
Metallocarboxypeptidases_(EC_3.4.17.-)	1
Methicillin_resistance_in_Staphylococci	-1
Methionine_Biosynthesis	1
Methionine_Degradation	2
Methionine_Salvage	-1
Methylcitrate_cycle	C
Methylglyoxal_Metabolism	-1
Methylthiotransferases	1.0100
Mevalonate_Branch_of_Isoprenoid_Biosynthesis	1
Molybdenum_cofactor_biosynthesis	1
Muconate_lactonizing_enzyme_family	1
Multi-subunit_cation_antiporter	1
Murein_Hydrolases	2.3
Mycobacterium_virulence_operon_involved_in_DNA_transcription	1.x
Mycobacterium_virulence_operon_involved_in_protein_synthesis_(LSU_ribosomal_proteins)	1
Mycobacterium_virulence_operon_involved_in_protein_synthesis_(SSU_ribosomal_proteins)	1.x
N-Acetyl-Galactosamine_and_Galactosamine_Utilization	-1
N-linked_Glycosylation_in_Bacteria	-1
NAD_and_NADP_cofactor_biosynthesis_global	C.x.ASPOX
NhaA,_NhaD_and_Sodium-dependent_phosphate_transporters	1
Niacin-Choline_transport_and_metabolism	1
Nitrate_and_nitrite_ammonification	2
Nitrosative_stress	3
Nonmevalonate_Branch_of_Isoprenoid_Biosynthesis	1
Nucleoside_triphosphate_pyrophosphohydrolase_MazG	1.110
Nudix_proteins_(nucleoside_triphosphate_hydrolases)	1
NusA-TFII_Cluster	7
One-carbon_metabolism_by_tetrahydropterines	9
Osmoregulation	1
Oxidative_stress	1
Oxygen_and_light_sensor_PpaA-PpsR	-1
Pentose_phosphate_pathway	1
Peptide_methionine_sulfoxide_reductase	1
Peptidoglycan_Biosynthesis	1
Peptidoglycan_biosynthesis--gjo	1
Peptidoglycan_lipid_II_flippase	1
Periplasmic_disulfide_interchange	1
Persister_Cells	1.x
Petrobactin-mediated_iron_uptake_system	1
Phage_packaging_machinery	2
Phage_tail_proteins	6
Phage_tail_proteins_2	6
Phenylalanine_and_Tyrosine_Branches_from_Chorismate	1
Phenylpropionate_Degradation	2
PhoR-PhoB_two-component_regulatory_system	9
Phosphate_metabolism	6
Phosphoglycerate_mutase_protein_family	1
Photorespiration_(oxidative_C2_cycle)	-1
Plasmid_replication	-1
Polyadenylation_bacterial	-1
Polyhydroxybutyrate_metabolism	2
Polyphosphate	1
Possible_new_toxin-antitoxin_system_including_DivIC	2
Potassium_homeostasis	2
Programmed_frameshift	8
Proline,_4-hydroxyproline_uptake_and_utilization	?
Proline_Synthesis	1
Propanediol_utilization	-1
Propionate-CoA_to_Succinate_Module	1
Proteasome_archaeal	5
Protection_from_Reactive_Oxygen_Species	1
Protein-L-isoaspartate_O-methyltransferase	1
Protein_chaperones	1.0
Protein_deglycation	1
Protein_degradation	1
Proteolysis_in_bacteria,_ATP-dependent	5
Proteorhodopsin	-1
Protocatechuate_branch_of_beta-ketoadipate_pathway	1.xx
Proton-dependent_Peptide_Transporters	1
Purine_Utilization	2.29
Purine_conversions	4.11103106
Purine_salvage_cluster	2
Putative_sugar_ABC_transporter_(ytf_cluster)	-1
Putrescine_utilization_pathways	2
Pyridoxin_(Vitamin_B6)_Biosynthesis	6.0
Pyruvate_Alanine_Serine_Interconversions	2.0
Pyruvate_metabolism_I:_anaplerotic_reactions,_PEP	1
Pyruvate_metabolism_II:_acetyl-CoA,_acetogenesis_from_pyruvate	2
Queuosine-Archaeosine_Biosynthesis	4.010
Quinate_degradation	3
Quinone_oxidoreductase_family	1
RNA_3'-terminal_phosphate_cyclase	1
RNA_methylation	1
RNA_modification_and_chromosome_partitioning_cluster	2.x
RNA_polymerase_bacterial	1.010
RNA_processing_and_degradation,_bacterial	1
RNA_pseudouridine_syntheses	1
Rad50-Mre11_DNA_repair_cluster	1.x
RecA_and_RecX	1
Recycling_of_Peptidoglycan_Amino_Acids	1.1
Redox-dependent_regulation_of_nucleus_processes	2
Resistance_to_Vancomycin	X
Resistance_to_fluoroquinolones	9
Respiratory_dehydrogenases_1	1.114
Rhamnose_containing_glycans	7
Riboflavin,_FMN_and_FAD_metabolism	A
Riboflavin,_FMN_and_FAD_metabolism_in_plants	A
Riboflavin_synthesis_cluster	1.x
Ribonuclease_H	1.110
Ribonucleases_in_Bacillus	-1
Ribosomal_protein_S12p_Asp_methylthiotransferase	-1
Ribosomal_protein_S5p_acylation	1.111
Ribosome_LSU_bacterial	1
Ribosome_activity_modulation	1
Ribosome_recycling_related_cluster	2.x
Rubrerythrin	9
RuvABC_plus_a_hypothetical	1.x
S-methylmethionine	1
Salicylate_and_gentisate_catabolism	2
Septum_site-determining_cluster_Min	1.x
Serine-glyoxylate_cycle	3.?
Serine_Biosynthesis	2.x
Sex_pheromones_in_Enterococcus_faecalis_and_other_Firmicutes	-1
Sialic_Acid_Metabolism	1.0
Siderophore_Enterobactin	8
SigmaB_stress_responce_regulation	8.1?
Signal_peptidase	3
Single-Rhodanese-domain_proteins	1
Sporulation-associated_proteins_with_broader_functions	1.100
Staphylococcal_pathogenicity_islands_SaPI	-1
Staphylococcal_phi-Mu50B-like_prophages	-1
Stationary_phase_repair_cluster	9.x
Stringent_Response,_(p)ppGpp_metabolism	1
Succinate_dehydrogenase	1
Sulfur_oxidation	-1
TCA_Cycle	3
TRAP_Transporter_collection	1
Teichoic_and_lipoteichoic_acids_biosynthesis	-1
Terminal_cytochrome_C_oxidases	3.I/III
Terminal_cytochrome_d_ubiquinol_oxidases	1
Terminal_cytochrome_oxidases	1
Tetracycline_resistance,_ribosome_protection_type	-1
Tetracycline_resistance,_ribosome_protection_type,_too	-1
Thiamin_biosynthesis	2
Thioredoxin-disulfide_reductase	1
Threonine_anaerobic_catabolism_gene_cluster	-1
Threonine_and_Homoserine_Biosynthesis	1.1
Ton_and_Tol_transport_systems	-1
Toxin-antitoxin_replicon_stabilization_systems	1.x
Transcription_factors_bacterial	1
Transcription_initiation,_bacterial_sigma_factors	1
Transcription_repair_cluster	9
Translation_elongation_factor_G_family	4
Translation_elongation_factor_P_lysylation	-1
Translation_elongation_factors_bacterial	1.1
Translation_initiation_factors_bacterial	1.110
Translation_termination_factors_bacterial	1.13
Trehalose_Biosynthesis	1.1
Trehalose_Uptake_and_Utilization	4.0
Triacylglycerol_metabolism	3
Tryptophan_synthesis	3
Twin-arginine_translocation_system	7
Two-component_sensor_regulator_linked_to_Carbon_Starvation_Protein_A	-1
UDP-N-acetylmuramate_from_Fructose-6-phosphate_Biosynthesis	A
USS-DB-7	-1
Ubiquinone_Menaquinone-cytochrome_c_reductase_complexes	1
Unknown_carbohydrate_utilization_(_cluster_Ydj_)	-1
Unspecified_monosaccharide_transport_cluster	-1
Uptake_of_selenate_and_selenite	1.1
Uracil-DNA_glycosylase	1
Urea_decomposition	1
Urease_subunits	1.2
Utilization_of_glutathione_as_a_sulphur_source	-1
WhiB_and_WhiB-type_regulatory_proteins_	6
YcfH	1
YjeE	1.0110
ar-104-EC_Molybdenum_cofactor_biosynthesis_moaABCDE	9.x
ar-431-EC_Molybdopterin-guanine_dinucleotide_biosynthesis	2.x
cAMP_signaling_in_bacteria	1.307
carbazol_degradation_cluster	-1
dTDP-rhamnose_synthesis	2.0
mnm5U34_biosynthesis_bacteria	1
n-Phenylalkanoic_acid_degradation	-1
p-Hydroxybenzoate_degradation	1
pVir_Plasmid_of_Campylobacter	-1
pyrimidine_conversions	1
riboflavin_to_FAD	3x
tRNA_aminoacylation,_Ala	1.00
tRNA_aminoacylation,_Arg	1.00
tRNA_aminoacylation,_Asp_and_Asn	2.1
tRNA_aminoacylation,_Cys	1
tRNA_aminoacylation,_Glu_and_Gln	2.01
tRNA_aminoacylation,_Gly	1
tRNA_aminoacylation,_His	1
tRNA_aminoacylation,_Ile	1.00
tRNA_aminoacylation,_Leu	1.00
tRNA_aminoacylation,_Lys	2.00
tRNA_aminoacylation,_Met	1.00
tRNA_aminoacylation,_Phe	1.00
tRNA_aminoacylation,_Ser	1.00
tRNA_aminoacylation,_Thr	1.00
tRNA_aminoacylation,_Trp	1.00
tRNA_aminoacylation,_Tyr	1.00
tRNA_aminoacylation,_Val	1.00
tRNA_nucleotidyltransferase	1
tRNA_processing	1
tRNA_splicing	-1
tRNAs	1