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revision 1.6, Thu Dec 22 00:52:43 2005 UTC revision 1.10, Thu Apr 13 10:45:03 2006 UTC
# Line 51  Line 51 
51  external        sp      4  external        sp      4
52  external        uni     1.3  external        uni     1.3
53  external        kegg    1  external        kegg    1
54  subsystems      trusted 8  subsystems      trusted 20
 2-isocapryloyl-3R-hydroxymethyl-gamma-butyrolactone_and_other_bacterial_morphogens      master:OlgaV  
 ABC_transporter_alkylphosphonate_(TC_3.A.1.9.1) master:MattC  
 ABC_transporter_arabinose_(TC_3.A.1.2.2)        master:MattC  
 ABC_transporter_branched-chain_amino_acid_(TC_3.A.1.4.1)        master:MattC  
 ABC_transporter_dipeptide_(TC_3.A.1.5.2)        master:MattC  
 ABC_transporter_ferric_enterobactin_(TC_3.A.1.14.2)     master:MattC  
 ABC_transporter_ferrichrome_(TC_3.A.1.14.3)     master:MattC  
 ABC_transporter_galactose_(TC_3.A.1.2.3)        master:MattC  
 ABC_transporter_glutamate_aspartate_(TC_3.A.1.3.4)      master:MattC  
 ABC_transporter_glutamine_(TC_3.A.1.3.2)        master:MattC  
 ABC_transporter_glycerol_(TC_3.A.1.1.3) master:MattC  
 ABC_transporter_heme_(TC3.A.1.107.1)    master:MattC  
 ABC_transporter_histidine_lysine_arginine_ornithine_(TC_3.A.1.3.1)      master:MattC  
 ABC_transporter_iron(III)_dicitrate_(TC_3.A.1.14.1)     master:MattC  
 ABC_transporter_L-proline_glycine_betaine_(TC_3.A.1.12.1)       master:MattC  
 ABC_transporter_macrolide       master:MattC  
 ABC_transporter_maltose master:MattC  
 ABC_transporter_molybdenum_(TC_3.A.1.8.1)       master:MattC  
 ABC_transporter_nickel_(TC_3.A.1.5.3)   master:MattC  
 ABC_transporter_oligopeptide_(TC_3.A.1.5.1)     master:MattC  
 ABC_transporter_peptide_(TC_3.A.1.5.5)  master:MattC  
 ABC_transporter_phosphate_(TC_3.A.1.7.1)        master:MattC  
 ABC_transporter_polyamine_putrescine_spermidine_(TC_3.A.1.11.1) master:MattC  
 ABC_transporter_putrescine_(TC_3.A.1.11.2)      master:MattC  
 ABC_transporter_ribose_(TC_3.A.1.2.1)   master:MattC  
 ABC_transporter_tungstate_(TC_3.A.1.6.2)        master:gjo  
 Accessory_Gene_Regulator        master:jcassat  
 Acetogenesis_from_Pyruvate      master:LienC_UCSD  
 Alanine_Biosynthesis    master:Straw  
 Alkaloid_biosynthesis_from_L-lysine     master:OlgaV  
 Alkaloid_biosynthesis_from_putrescine   master:OlgaV  
 Alkaloid_biosynthesis_from_tyrosine     master:OlgaV  
 Alkanesulfonate_assimilation    master:OlgaV  
 Alkanesulfonates_Utilization    master:RobE  
 Allantoin_degradation   master:MattC  
 Ammonia_assimilation    master:EdF  
 Anaerobic_benzoate_metabolism   master:MatthewH_UFL  
 Anaerobic_respiratory_reductases        master:OlgaV  
 Anthocyanin_biosynthesis        master:OlgaV  
 Anthracycline_biosynthesis      master:OlgaV  
 Apigenin_derivatives    master:OlgaV  
 Archaeal_Flagellum      master:RickS  
 Arginine_Biosynthesis   RickS  
 Arginine_Putrescine_and_4-aminobutyrate_degradation     master:MattC  
 Aromatic_Amin_Catabolism        master:OlgaV  
 Aromatic_amino_acid_degradation master:OlgaV  
 Asp-Glu-tRNA(Asn-Gln)_transamidation    master:gjo  
 Auxin_biosynthesis      master:OlgaV  
 Auxin_degradation       master:OlgaV  
 Bacterial_Apoptosis     master:KaitlynH  
 Bacterial_Cell_Division master:RickS  
 Bacterial_Chemotaxis    master:RickS  
 Bacterial_motility:Gliding      master:OlgaV  
 Benzoate_catabolism     master:changhaobi-ufl  
 Benzoate_degradation    master:OlgaV  
 Betaine_biosynthesis    master:MattC  
 Biflavanoid_biosynthesis        master:OlgaV  
 Bilin_Biosynthesis      master:OlgaZ  
 Biotin_biosynthesis     master:rodionov  
 Biphenyl_Degradation    master:OlgaV  
 Bis-_and_Tris-Indole_alkaloids  master:OlgaV  
 Branched-Chain_Amino_Acid_Biosynthesis  master:RossO  
 Bsub-Spore-Coat master:RickS  
 Butyrate_and_Butanol_Acetone_fermentation       master:SouravB_UCSD  
 Caffeic_acid_derivatives        master:OlgaV  
 Calvin-Benson_cycle     master:SvetaG  
 Cannabinoid_biosynthesis        master:OlgaV  
 Capsular_heptose_biosynthesis   master:OlgaZ  
 Capsular_polysaccharide_biosynthesis_in_Staphylococcus  master:JenZ  
 Capsular_surface_virulence_antigen_loci master:JenZ  
 Carbon_monoxide_dehydrogenases  master:rodionov  
 Carboxysome     master:MalgorzataG_UFL  
 carnitine_metabolism    master:MattC  
 Carotenoids     master:OlgaV  
 Catechol_branch_of_beta-ketoadipate_pathway     master:OlgaV  
 CbiQO-type_ABC_transporter_systems      master:rodionov  
 Central_meta-cleavage_pathway_of_aromatic_compound_degradation  master:OlgaV  
 Chloroaromatic_degradation_pathway      master:OlgaV  
 Chlorophyll_Biosynthesis        master:VeronikaV  
 Chlorophyll_Degradation master:SvetaG  
 Cholera_toxin   master:VeronikaV  
 Choline_Transport       master:RobE  
 Chorismate_Synthesis    master:VeronikaV  
 Citrate_Metabolism,_Transport,_and_Regulation   master:JenZ  
 Clavulanic_acid_biosynthesis    master:OlgaV  
 CMP-N-acetylneuraminate_Biosynthesis    master:OlgaZ  
 Cobalamin_synthesis     master:gjo  
 Coenzyme_A_Biosynthesis master:AndreiO  
 Coenzyme_A_Biosynthesis_in_Pathogens    master:AndreiO  
 Coenzyme_F420-H2_dehydrogenase_(methanophenazine)       master:gjo  
 Coenzyme_F420_hydrogenase       master:gjo  
 Coenzyme_F420_synthesis master:gjo  
 coenzyme_M_biosynthesis master:AdamF  
 Coenzyme_PQQ_synthesis  master:gjo  
 Colanic_acid_biosynthesis       master:JenZ  
 Coumarin_biosynthesis   master:OlgaV  
 Cyanobacterial_Circadian_Clock  master:OlgaZ  
 Cyanobacterial_CO2_uptake       master:OlgaV  
 Cyanophycin_metabolism  master:MikeR  
 cysteine_biosynthesis   master:RobE  
 Cytochrome_B6-F_complex master:Sveta  
 Cytochrome_oxidase_assembly_factors     master:SvetaG  
 Cytolethal_distending_toxin_of_Campylobacter_jejuni     master:OlgaZ  
 Cytoskeleton    master:JenZ  
 Cytotoxic_Polyacetylenes        master:OlgaV  
 D-alanyl_lipoteichoic_acid_Biosynthesis master:OlgaZ  
 D-arabinose_degradation master:MattC  
 D-galactarate_degradation       master:MattC  
 D-galacturonate_degradation     master:MattC  
 D-glucarate_degradation master:MattC  
 D-tyrosyl-tRNA(Tyr)_deacylase   master:gjo  
 De_Novo_Purine_Biosynthesis     master:RossO  
 De_Novo_Pyrimidine_Synthesis    master:RossO  
 Dehydrogenase_complexes master:VeronikaV  
 Denitrification master:rodionov  
 Differentiation_in_bacteria:transcription_factors_and_signaling_systems master:OlgaV  
 DNA-replication master:RickS  
 DNA_repair,_bacterial   master:gjo  
 DNA_repair_and_recombination_eukaryotic master:gjo  
 DNA_Repair_Base_Excision        master:MikeK  
 dTDP-rhamnose_synthesis master:MikeK  
 Embden-Meyerhof_and_Gluconeogenesis     master:SvetaG  
 Embden-Meyerhof_and_Gluconeogenesis_Archaeal    master:SvetaG  
 Entner-Doudoroff_Pathway        master:SvetaG  
 Ethanolamine_utilization        master:gjo  
 F0F1-type_ATP_synthase  master:RickS  
 Fatty_Acid_Biosynthesis_FASII   master:AndreiO  
 fatty_acid_metabolism   master:MattC  
 fatty_acid_oxidation_pathway    master:MattC  
 Fe-S_cluster_assembly   master:rodionov  
 Fermentations:_Lactate  master:SvetaG  
 Fermentations:_Mixed_acid       master:SvetaG  
 Flagellum       master:RickS  
 Flavanone_biosynthesis  master:OlgaV  
 FMN_and_FAD_biosynthesis        master:AndreiO  
 FMN_and_FAD_biosynthesis_in_pathogens   master:AndreiO  
 Folate_Biosynthesis     master:vcrecy  
 Formate_dehydrogenase   master:gjo  
 Formate_hydrogenase     master:OlgaV  
 Fructose-bisphosphate_aldolase_protein_family   master:SvetaG  
 Fucose_and_rhamnose_degradation master:MattC  
 Fungal_cytostatics      master:OlgaV  
 Fungal_differentiation_factors  master:OlgaV  
 Galactitol_degradation  master:MattC  
 Galactose_degradation   master:MattC  
 General_secretory_pathway_(Sec-SRP)_complex_(TC_3.A.5.1.1)      master:MattC  
 Glutamate,_aspartate_and_asparagine_biosynthesis        master:MattC  
 Glutamate_biosynthesis  master:MattC  
 Glutamyl_peptidase?     master:RamyA  
 Glutathione_Redox_Metabolism    master:Neema_UCSD  
 Glycerol_fermenation_to_1,3-propanediol master:gjo  
 Glycerol_Metabolism     master:MattC  
 Glycerolipid_and_glycerphospholipid_metabolism  master:VasiliyP_UCSD  
 Glycine_cleavage_system master:MattC  
 Glycine_reductase,_sarcosine_reductase_and_betaine_reductase    master:gjo  
 Glycine_synthesis       master:MikeK  
 glyoxylate_degradation  master:MattC  
 Glyoxylate_Synthesis    master:RickS  
 Gram-Positive_Extracellular_Nucleases   master:RamyA  
 gram_plus_late_competence       master:alexS  
 GroEL_GroES     master:MikeK  
 Heavy_metal_ion_sensors_and_exporters   master:JenZ  
 Heme-bound_Iron_Scavenge_Pathway        master:RickS  
 Hexitol_degradation     master:MattC  
 Histidine_Biosynthesis  master:RossO  
 Histidine_Degradation   master:RossO  
 HMG_CoA_Synthesis       master:VeronikaV  
 Homogentisate_pathway_of_aromatic_compound_degradation  master:OlgaV  
 hpa_catabolic_pathway   master:YakovK  
 Hydrogenases    master:OlgaV  
 Inorganic_Sulfur_Assimilation   master:ChristianR  
 Inositol_catabolism     master:VeronikaV  
 Intercellular_adhesion_SA       master:MattC  
 Isoleucine_degradation  master:OlgaZ  
 Isoprenoid_Biosynthesis master:OlgaZ  
 KDO2-Lipid_A_biosynthesis       master:OlgaZ  
 Ketogluconate_metabolism        master:MattC  
 L-ascorbate_degradation master:MattC  
 Lactose_degradation     master:MattC  
 Leucine_Biosynthesis_v2 master:AdamF  
 Leucine_Degradation_and_HMG-CoA_Metabolism      master:VeronikaV  
 Lignine_biosynthesis    master:OlgaV  
 linker_unit-arabinogalactan_synthesis   master:NJ  
 Lipid_A_biosynthesis    master:OlgaZ  
 Lipid_A_modifications   master:OlgaZ  
 Lipoic_acid_metabolism  master:gjo  
 Lipoteichoic_acid_biosynthesis  master:RamyA  
 Listeria_Pathogenicity_Island_LIPI-1_extended   master:SvetaG  
 Listeria_surface_proteins:_Internalin-like_proteins     master:SvetaG  
 Listeria_surface_proteins:_LPXTG_motif  master:SvetaG  
 LMPTP_YfkJ_cluster      master:AndreiO  
 LMPTP_YwlE_cluster      master:AndreiO  
 LOS_core_oligosaccharide_biosynthesis   master:OlgaZ  
 Lysine_Biosynthesis_DAP_Pathway master:AndreiO  
 Malonate_decarboxylase  master:VeronikaV  
 Mannose-sensitive_hemagglutinin_type_4_pilus    master:RobE  
 Mannose_and_fructose_metabolism master:HanYuC_UCSD  
 mannose_and_GDP-mannose_metabolism      master:MattC  
 Membrane-bound_Ni,_Fe-hydrogenase       master:rodionov  
 Menaquinone_and_Phylloquinone_Biosynthesis      master:OlgaZ  
 Menaquinone_Biosynthesis        master:RickS  
 Mercury_resistance_operon       master:JenZ  
 Methane_metabolism      master:MikeR  
 Methanogenesis  master:gjo  
 Methanogenesis_from_methylated_compounds        master:gjo  
 Methanophenazine_hydrogenase    master:gjo  
 methanopterin_biosynthesis      master:AdamF  
 Methionine_Biosynthesis master:rodionov  
 Methionine_Salvage      master:gjo  
 Methylcitrate_cycle     master:MattC  
 Methylglyoxal_Metabolism        master:OlgaZ  
 MLST    master:RobE  
 Molybdopterin_biosynthesis      master:JenZ  
 mycolic_acid_synthesis  master:NJ  
 N-Acetyl-D-Glucosamine_Utilization      master:OlgaZ  
 N-heterocyclic_aromatic_compound_degradation    master:OlgaV  
 N-linked_Glycosylation_in_Bacteria      master:OlgaZ  
 n-Phenylalkanoic_acid_degradation       master:OlgaV  
 Na(+)-translocating_NADH-quinone_oxidoreductase_and_rnf-like_group_of_electron_transport_complexes      master:OlgaV  
 NAD_and_NADP_cofactor_biosynthesis_global       master:AndreiO  
 NAD_and_NADP_cofactor_biosynthesis_in_pathogens master:AndreiO  
 NAD_and_NADP_paper      master:SvetaG  
 NAD_and_NADP_tutorial_10        master:AndreiO  
 Naphtalene_and_antracene_degradation    master:OlgaV  
 NiFe_hydrogenase_maturation     master:gjo  
 Nitrate_and_nitrite_ammonification      master:rodionov  
 Nitrosative_stress      master:rodionov  
 NusA-TFII_Cluster       master:gjo  
 O-linked_flagella_Glycosylation master:OlgaZ  
 Octadecanoids   master:OlgaV  
 Osmotically_activated_L-carnitine_ABC_transporter_in_Listeria   master:JenZ  
 Oxidative_stress        master:OlgaV  
 Oxidative_stress_(animal_systems)       master:OlgaV  
 Oxidative_stress_in_bacteria    master:OlgaV  
 p-Hydroxybenzoate_degradation   master:OlgaV  
 P-type_ATPase_transporter_potassium_(TC_3.A.3.7.1)      master:MattC  
 P_uptake_(cyanobacteria)        master:acm_at_mit  
 Pentose_phosphate_pathway       master:SvetaG  
 Peptidoglycan_Biosynthesis      master:RickS  
 Phenylacetate_pathway_of_aromatic_compound_degradation  master:OlgaV  
 Phenylalanine_synthesis master:MikeK  
 Phenylpropanoid_compound_degradation    master:OlgaV  
 Phenylpropanoids_general_biosynthesis   master:OlgaV  
 Phenylpropionate_Degradation    master:OlgaV  
 Phosphoglycerate_mutase_protein_family  master:SvetaG  
 Phosphotransferase_enzyme_II_-_Glucose_class_permease   master:JenZ  
 Phosphotransferase_enzyme_II_-_Lactose_class_permease   master:JenZ  
 Phosphotransferase_enzyme_II_-_Mannitol_class_permease  master:JenZ  
 Phosphotransferase_enzyme_II_-_Mannose_family_permease  master:JenZ  
 Photosystem_I   master:SvetaG  
 Photosystem_II  master:SvetaG  
 Phycobilisome   master:OlgaZ  
 Phytoalexin_biosynthesis        master:OlgaV  
 Phytochromes    master:OlgaZ  
 Phytosterol_biosynthesis        master:OlgaV  
 Plastoquinone_Biosynthesis      master:OlgaZ  
 Polyadenylation_bacterial       master:gjo  
 Polyamine_Metabolism    master:InesT_UCSD  
 polyisoprenoid_biosynthesis     master:MattC  
 polyprenyl_synthesis    master:NJ  
 Porphyrin,_Heme,_and_Siroheme_Biosynthesis      master:SvetaG  
 ppGpp_biosynthesis      master:MikeK  
 Proline_Catabolism      master:laszloC  
 Proline_degradation     master:unknown  
 Proline_degradation1    master:unknown  
 Proline_Synthesis       master:RickS  
 Propanediol_utilization master:gjo  
 Prophage-encoded_Exotoxins      master:RamyA  
 Prophage_lysogenic_conversion_modules   master:RamyA  
 Proteasome_archaeal     master:gjo  
 Proteasome_eukaryotic   master:gjo  
 Protection_from_Reactive_Oxygen_Species master:MikeK  
 Protein_Acetylation_and_Deacetylation_in_Bacteria       master:AndreiO  
 Protein_degradation     master:gjo  
 Proteolysis_in_bacteria,_ATP-dependent  master:OlgaZ  
 Protocatechuate_branch_of_beta-ketoadipate_pathway      master:OlgaV  
 Protozoan_cytostatics_and_differentiation_factors       master:OlgaV  
 Pterin_biosynthesis     master:vcrecy  
 Purine_conversions      master:OlgaV  
 pyrimidine_conversions  master:RossO  
 Pyrroloquinoline_Quinone_biosynthesis   master:OlgaZ  
 Pyruvate:ferredoxin_oxidoreductase      master:SvetaG  
 Pyruvate_Alanine_Serine_Interconversions        master:JasonS_UCSD  
 Pyruvate_metabolism_I:_anaplerotic_reactions,_PEP       master:SvetaG  
 Queuosine-Archaeosine_Biosynthesis      master:vcrecy  
 Quinate_degradation     master:OlgaV  
 Quinolinic_acid_and_its_derivatives     master:OlgaV  
 Quorum_Sensing:_Autoinducer-2_Synthesis master:AndrewJ  
 Redox-dependent_regulation_of_nucleus_processes master:OlgaV  
 Resistance_to_fluoroquinolones  master:MattC  
 Resistance_to_Vancomycin        master:MattC  
 Respiratory_Complex_I   master:OlgaV  
 Respiratory_dehydrogenases_1    master:OlgaV  
 Riboflavin_metabolism   master:rodionov  
 Ribonuclease_P_archaeal_and_eukaryal    master:gjo  
 Ribonucleotide_reduction        master:rodionov  
 Ribose_and_deoxyribose_phosphate_metabolism     master:MattC  
 Ribosome_biogenesis_bacterial   master:gjo  
 Ribosome_LSU_bacterial  master:gjo  
 Ribosome_LSU_chloroplast        master:gjo  
 Ribosome_LSU_eukaryotic_and_archaeal    master:gjo  
 Ribosome_LSU_mitochondrial      master:gjo  
 Ribosome_SSU_bacterial  master:gjo  
 Ribosome_SSU_chloroplast        master:gjo  
 Ribosome_SSU_eukaryotic_and_archaeal    master:gjo  
 Ribosome_SSU_mitochondrial      master:gjo  
 RNA_polymerase_archaeal master:gjo  
 RNA_polymerase_archaeal_initiation_factors      master:gjo  
 RNA_polymerase_bacterial        master:gjo  
 RNA_polymerase_chloroplast      master:gjo  
 RNA_polymerase_I        master:gjo  
 RNA_polymerase_II       master:gjo  
 RNA_polymerase_II_initiation_factors    master:gjo  
 RNA_polymerase_III      master:gjo  
 Rrf2_family_transcriptional_regulators  master:rodionov  
 Salicylate_ester_degradation    master:OlgaV  
 Salicylic_acid_biosynthesis1    master:OlgaV  
 Selenocysteine_metabolism       master:gjo  
 Serine_Biosynthesis     master:MikeK  
 Siderophore_Aerobactin_and_Ferrichrome_Biosynthesis     master:MikeK  
 Siderophore_enterobactin_biosynthesis   master:MattC  
 Siderophore_enterobactin_biosynthesis_and_ferric_enterbactin_transport  master:MattC  
 Siderophore_Yersiniabactin_Biosynthesis master:MikeK  
 SLO-NADGH_Locus master:RamyA  
 Sodium_Hydrogen_Antiporter      master:JenZ  
 Soluble_cytochromes_and_functionally_related_electron_carriers  master:OlgaV  
 SpeB-SpeF_extended_regulon      master:RamyA  
 Sphingolipid_biosynthesis       master:JorgeF  
 Spliceosome     master:gjo  
 Spore_Coat      master:RickS  
 Steroid_sulfates        master:OlgaV  
 Streptococcal_Hyaluronic_Acid_Capsule   master:RamyA  
 Streptococcal_Mga_Regulon       master:RamyA  
 Streptococcus_pyogenes_Transcription_Regulators master:RamyA  
 Streptococcus_pyogenes_Virulome master:RamyA  
 Streptolysin_S_Biosynthesis_and_Transport       master:RamyA  
 Streptomycin_biosynthesis       master:OlgaV  
 Suberine_biosynthesis   master:OlgaV  
 Succinate_dehydrogenase master:OlgaV  
 Sucrose_Metabolism      master:MattC  
 Sulfate_assimilation    master:MattC  
 Sulfate_to_Sulfide      master:RobE  
 Sulfur_Metabolism       master:RobE  
 Tannin_biosynthesis     master:OlgaV  
 Taurine_Utilization     master:RobE  
 TCA_Cycle       master:OlgaV  
 Teichoic_acid_Biosynthesis      master:OlgaZ  
 Terminal_cytochrome_C_oxidases  master:OlgaV  
 Terminal_cytochrome_oxidases    master:OlgaV  
 Terpen_biosynthesis     master:OlgaV  
 The_Tartronate_Semialdehyde_Hub master:RossO  
 Thiamin_biosynthesis    master:rodionov  
 Thioredoxin-disulfide_reductase master:gjo  
 Threonine_degradation   master:OlgaV  
 Threonine_synthesis     master:MikeK  
 Tocopherol_Biosynthesis master:OlgaZ  
 Toluene_degradation     master:OlgaV  
 Transcription_factors_bacterial master:gjo  
 Transcription_factors_cyanobacterial_RpoD-like_sigma_factors    master:gjo  
 Translation_elongation_factors_eukaryotic_and_archaeal  master:gjo  
 Translation_factors_bacterial   master:gjo  
 Translation_initiation_factors_eukaryotic_and_archaeal  master:gjo  
 Transport_of_Nickel_and_Cobalt  master:rodionov  
 Trehalose_biosynthesis  master:MattC  
 Triacylglycerol_biosynthesis    master:unknown  
 Triacylglycerol_degradation     master:unknown  
 Tricarballylate_Utilization     master:RossO  
 tRNA_aminoacylation     master:gjo  
 tRNA_aminoacylation,_mitochondrial      master:gjo  
 tRNA_processing master:gjo  
 tRNA_splicing   master:gjo  
 Tryptophan_synthesis    master:VeronikaV  
 Tyrosine_synthesis      master:MikeK  
 Ubiquinone_Biosynthesis master:OlgaZ  
 Ubiquinone_Menaquinone-cytochrome_c_reductase_complexes master:OlgaV  
 UDP-N-acetylmuramate_from_Fructose-6-phosphate_Biosynthesis     master:vasiliyP  
 Universal_GTPases       master:gjo  
 Urea_decomposition      master:rodionov  
 Utilization_of_glutathione_as_a_sulphur_source  master:OlgaV  
 V-Type_ATP_synthase     master:RickS  
 Valine_Biosynthesis     master:Straw  
 Valine_degradation      master:OlgaZ  
 Vibrio_Experimental_Type_III_secretion_system   master:JanelleT  
 //  
55  END  END
56  ;  ;
57      return split(/\n/,$x);      my @parms = split(/\n/,$x);
58        my $fig = new FIG;
59        my @trusted_subsystems = map { my $sub = $_; my $curr = $fig->subsystem_curator($sub);
60                                       "$sub\t$curr\n"
61                                     }
62                                 grep { $fig->usable_subsystem($_) }
63                                 $fig->all_subsystems;
64        push(@parms,@trusted_subsystems,"//\n");
65        return @parms;
66  }  }
67    
68    
69  sub choose_best_assignment {  sub choose_best_assignment {
70      my($fig,$parms,$pegs,$external_ids) = @_;      my($fig,$parms,$pegs,$external_ids,$ignore) = @_;
71      my($peg,$id);      my($peg,$id);
72    
73      my $functions = {};      my $functions = {};
# Line 451  Line 75 
75      {      {
76          &load_peg_function($fig,$parms,$peg,$functions);          &load_peg_function($fig,$parms,$peg,$functions);
77      }      }
78        my @tmp = keys(%$functions);
79    #   print &Dumper(['peg check',\@tmp,$functions]);
80    
81        if ((@tmp == 1) && (@$pegs >= 5)) { return $tmp[0] }
82    
83      foreach $id (@$external_ids)      foreach $id (@$external_ids)
84      {      {
# Line 490  Line 118 
118    
119  #       print STDERR "picking from set ",&Dumper($set);  #       print STDERR "picking from set ",&Dumper($set);
120          ($poss_function,$best_source) = &pick_specific($fig,$parms,$set,$functions);          ($poss_function,$best_source) = &pick_specific($fig,$parms,$set,$functions);
121  #       print STDERR "picked $best_function from $best_source\n";  #       print STDERR "picked $poss_function from $best_source\n";
122          push(@scored,[$score,$poss_function,$best_source]);          push(@scored,[$score,$poss_function,$best_source]);
123      }      }
124      @scored = sort { $b->[0] <=> $a->[0] } @scored;      @scored = sort { $b->[0] <=> $a->[0] } @scored;
# Line 529  Line 157 
157      my($best_func,$best_score,$func,$x,$best_source);      my($best_func,$best_score,$func,$x,$best_source);
158    
159      $best_func  = "";      $best_func  = "";
160      $best_score = "";      $best_score = 0;
161      $best_source = "";      $best_source = "";
162    
163      foreach $func (@$set)      foreach $func (@$set)
# Line 617  Line 245 
245          }          }
246          foreach $tuple ($fig->mapped_prot_ids($peg))          foreach $tuple ($fig->mapped_prot_ids($peg))
247          {          {
248              if ($tuple->[0] =~ /^fig\|/)              if (($tuple->[0] =~ /^fig\|/) && $fig->is_real_feature($tuple->[0]))
249              {              {
250                  $pegs{$tuple->[0]} = 1;                  $pegs{$tuple->[0]} = 1;
251              }              }

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