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revision 1.4, Mon Dec 5 19:06:30 2005 UTC revision 1.17, Wed Sep 10 20:09:55 2008 UTC
# Line 25  Line 25 
25  sub default_parms {  sub default_parms {
26    
27      my $x = <<END      my $x = <<END
 genome  198214.1        4       Shigella flexneri 2a str. 301  
 genome  198215.1        4       Shigella flexneri 2a str. 2457T  
 genome  216598.1        4       Shigella dysenteriae M131649  
 genome  216599.1        4       Shigella sonnei 53G  
 genome  630.2   4       Yersinia enterocolitica 8081  
 genome  633.2   4       Yersinia pseudotuberculosis (Livermore)  
 genome  187410.1        4       Yersinia pestis KIM  
 genome  214092.1        4       Yersinia pestis CO92  
 genome  229193.1        4       Yersinia pestis biovar Medievalis str. 91001  
 genome  273123.1        4       Yersinia pseudotuberculosis IP 32953  
 genome  594.1   4       Salmonella enterica subsp. enterica serovar Gallinarum  
 genome  99287.1 4       Salmonella typhimurium LT2  
 genome  119912.1        4       Salmonella enterica serovar Choleraesuis SC-B67  
 genome  209261.1        4       Salmonella enterica subsp. enterica serovar Typhi Ty2  
 genome  220341.1        4       Salmonella enterica subsp. enterica serovar Typhi str. CT18  
 genome  83333.1 4       Escherichia coli K12  
 genome  83334.1 4       Escherichia coli O157:H7  
 genome  155864.1        4       Escherichia coli O157:H7 EDL933  
 genome  199310.1        4       Escherichia coli CFT073  
 genome  216592.1        4       Escherichia coli 042  
 genome  216593.1        4       Escherichia coli E2348/69  
 genome  192222.1        4       Campylobacter jejuni subsp. jejuni NCTC 11168  
 genome  224308.1        2       Bacillus subtilis subsp. subtilis str. 168  
28  external        sp      4  external        sp      4
29    external        img     4
30  external        uni     1.3  external        uni     1.3
31  external        kegg    1  external        kegg    1
32  subsystems      trusted 8  external        gi      1
 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  
 //  
33  END  END
34  ;  ;
35      return split(/\n/,$x);  #
36    # TO PUT FIG ANNOTATIONS BACK IN ADD THE FOLLOWING LINE
37    #######################################################
38    #subsystems     trusted 20
39    #######################################################
40    # You may also improve things by adding lines like:
41    #
42    #genome 83333.1 15      Escherichia coli K12
43    #
44    #######################################################
45    
46        my @parms = split(/\n/,$x);
47        my $fig = new FIG;
48        my @trusted_subsystems = map { my $sub = $_; my $curr = $fig->subsystem_curator($sub);
49                                       "$sub\t$curr\n"
50                                     }
51                                 grep { $fig->usable_subsystem($_) }
52                                 $fig->all_subsystems;
53        push(@parms,@trusted_subsystems,"//\n");
54        return @parms;
55  }  }
56    
57    
58  sub choose_best_assignment {  sub choose_best_assignment {
59      my($fig,$parms,$pegs,$external_ids) = @_;      my($fig,$parms,$pegs,$external_ids,$ignore) = @_;
60      my($peg,$id);      my($peg,$id);
61    
62      my $functions = {};      my $functions = {};
# Line 451  Line 64 
64      {      {
65          &load_peg_function($fig,$parms,$peg,$functions);          &load_peg_function($fig,$parms,$peg,$functions);
66      }      }
67        my @tmp = keys(%$functions);
68        print STDERR &Dumper(['peg check',\@tmp,$functions]) if ($ENV{'DEBUG'} || $ENV{'VERBOSE'});
69    
70        if ((@tmp == 1) && (@$pegs >= 5)) { return $tmp[0] }
71    
72      foreach $id (@$external_ids)      foreach $id (@$external_ids)
73      {      {
# Line 467  Line 84 
84      if (! $func)                                           { return "hypothetical protein" }      if (! $func)                                           { return "hypothetical protein" }
85      if ($func =~ /^hypothetical (\S+ )?protein .*$/i)      { return "hypothetical protein" }      if ($func =~ /^hypothetical (\S+ )?protein .*$/i)      { return "hypothetical protein" }
86      if ($func =~ /^[a-zA-Z]{1,2}\d{2,5}( protein)?$/i)     { return "hypothetical protein" }      if ($func =~ /^[a-zA-Z]{1,2}\d{2,5}( protein)?$/i)     { return "hypothetical protein" }
87        if ($func =~ /^similar to ORF\d+$/)                    { return "hypothetical protein" }
88        if ($func =~ /^(Alr|As|All|Tlr|Tll|Glr|Blr|Slr|SEW|pANL)\d+( protein)?$/i) { return "hypothetical protein" }
89        if ($func =~ /^\d{5}/)                                 { return "hypothetical protein" }
90        if ($func =~ /unknown protein/)                        { return "hypothetical protein" }
91    
92      return $func;      return $func;
93  }  }
# Line 475  Line 96 
96      my($fig,$parms,$functions) = @_;      my($fig,$parms,$functions) = @_;
97      my($set,$score,$best_source,$poss_function);      my($set,$score,$best_source,$poss_function);
98      my(@scored);      my(@scored);
   
99      my @partitions = &SameFunc::group_funcs(keys(%$functions));      my @partitions = &SameFunc::group_funcs(keys(%$functions));
100      if ($ENV{'VERBOSE'}) {  print STDERR "partition: ",&Dumper(\@partitions,$functions); }      if ($ENV{'VERBOSE'}) {  print STDERR "partition: ",&Dumper(\@partitions,$functions); }
101    
102      foreach $set (@partitions)      foreach $set (@partitions)
103      {      {
104          $score = &score_set($set,$functions);          $score = &score_set($set,$functions);
105  #       print STDERR &Dumper([$score,$set]);          if ($ENV{'DEBUG'}) { print STDERR &Dumper([$score,$set]); }
106    
107  #       print STDERR "picking from set ",&Dumper($set);          if ($ENV{'DEBUG'}) { print STDERR "picking from set ",&Dumper($set); }
108          ($poss_function,$best_source) = &pick_specific($fig,$parms,$set,$functions);          ($poss_function,$best_source) = &pick_specific($fig,$parms,$set,$functions);
109  #       print STDERR "picked $best_function from $best_source\n";          if ($ENV{'DEBUG'}) { print STDERR "picked $poss_function from $best_source\n"; }
110          push(@scored,[$score,$poss_function,$best_source]);          push(@scored,[$score,$poss_function,$best_source]);
111      }      }
112      @scored = sort { $b->[0] <=> $a->[0] } @scored;      @scored = sort { $b->[0] <=> $a->[0] } @scored;
# Line 525  Line 145 
145      my($best_func,$best_score,$func,$x,$best_source);      my($best_func,$best_score,$func,$x,$best_source);
146    
147      $best_func  = "";      $best_func  = "";
148      $best_score = "";      $best_score = 0;
149      $best_source = "";      $best_source = "";
150    
151      foreach $func (@$set)      foreach $func (@$set)
# Line 575  Line 195 
195          {          {
196              $value += $_;              $value += $_;
197          }          }
   
198          my $subv = 0;          my $subv = 0;
199          my @subs = $fig->peg_to_subsystems($peg);          my @subs = ();
200            foreach my $sub ($fig->peg_to_subsystems($peg))
201            {
202                if (1) # (&solid_sub_assign($fig,$sub,$peg,$func))
203                {
204                    push(@subs,$sub);
205                }
206            }
207          my $sub;          my $sub;
208          my $in_sub = 0;          my $in_sub = 0;
209          foreach $sub (@subs)          foreach $sub (@subs)
# Line 596  Line 222 
222      }      }
223  }  }
224    
225    sub solid_sub_assign {
226        my($fig,$sub,$peg,$func) = @_;
227    
228        my $curator = $fig->subsystem_curator($sub);
229        $curator =~ s/^master://;
230        return ($fig->usable_subsystem($sub) && &made_by_curator($fig,$peg,$func,$curator));
231    }
232    
233    sub made_by_curator {
234        my($fig,$peg,$func,$curator) = @_;
235    
236        my @ann = $fig->feature_annotations($peg,"rawtime");
237        my $i;
238        my $funcQ = quotemeta $func;
239        for ($i=$#ann;
240             ($i >= 0) && (($ann[$i]->[2] !~ /$curator/) || ($ann[$i]->[3] !~ /Set \S+ function to\n$funcQ/s));
241             $i--) {}
242        return ($i >= 0);
243    }
244    
245  sub equivalent_ids {  sub equivalent_ids {
246      my($fig,$parms,$pegs) = @_;      my($fig,$parms,$pegs) = @_;
247      my($peg,@aliases,$alias,%external_ids,%pegs,$tuple);      my($peg,@aliases,$alias,%external_ids,%pegs,$tuple);
# Line 613  Line 259 
259          }          }
260          foreach $tuple ($fig->mapped_prot_ids($peg))          foreach $tuple ($fig->mapped_prot_ids($peg))
261          {          {
262              if ($tuple->[0] =~ /^fig\|/)              if (($tuple->[0] =~ /^fig\|/) && $fig->is_real_feature($tuple->[0]))
263              {              {
264                  $pegs{$tuple->[0]} = 1;                  $pegs{$tuple->[0]} = 1;
265              }              }

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