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revision 1.2, Sun Aug 14 01:47:51 2005 UTC revision 1.3, Wed Aug 17 12:24:43 2005 UTC
# Line 32  Line 32 
32  genome  192222.1        4       Campylobacter jejuni subsp. jejuni NCTC 11168  genome  192222.1        4       Campylobacter jejuni subsp. jejuni NCTC 11168
33  genome  224308.1        2       Bacillus subtilis subsp. subtilis str. 168  genome  224308.1        2       Bacillus subtilis subsp. subtilis str. 168
34  external        sp      4  external        sp      4
35  external        uni     2  external        uni     1.3
36  external        kegg    1  external        kegg    1
37  subsystems      trusted 8  subsystems      trusted 8
38  ABC_transporter_L-proline_glycine_betaine_(TC_3.A.1.12.1)       MattC  2-isocapryloyl-3R-hydroxymethyl-gamma-butyrolactone_and_other_bacterial_morphogens      master:OlgaV
39  ABC_transporter_alkylphosphonate_(TC_3.A.1.9.1) MattC  ABC_transporter_alkylphosphonate_(TC_3.A.1.9.1) master:MattC
40  ABC_transporter_arabinose_(TC_3.A.1.2.2)        MattC  ABC_transporter_arabinose_(TC_3.A.1.2.2)        master:MattC
41  ABC_transporter_branched-chain_amino_acid_(TC_3.A.1.4.1)        MattC  ABC_transporter_branched-chain_amino_acid_(TC_3.A.1.4.1)        master:MattC
42  ABC_transporter_dipeptide_(TC_3.A.1.5.2)        MattC  ABC_transporter_dipeptide_(TC_3.A.1.5.2)        master:MattC
43  ABC_transporter_ferric_enterobactin_(TC_3.A.1.14.2)     MattC  ABC_transporter_ferric_enterobactin_(TC_3.A.1.14.2)     master:MattC
44  ABC_transporter_ferrichrome_(TC_3.A.1.14.3)     MattC  ABC_transporter_ferrichrome_(TC_3.A.1.14.3)     master:MattC
45  ABC_transporter_galactose_(TC_3.A.1.2.3)        MattC  ABC_transporter_galactose_(TC_3.A.1.2.3)        master:MattC
46  ABC_transporter_glutamate_aspartate_(TC_3.A.1.3.4)      MattC  ABC_transporter_glutamate_aspartate_(TC_3.A.1.3.4)      master:MattC
47  ABC_transporter_glutamine_(TC_3.A.1.3.2)        MattC  ABC_transporter_glutamine_(TC_3.A.1.3.2)        master:MattC
48  ABC_transporter_glycerol_(TC_3.A.1.1.3) MattC  ABC_transporter_glycerol_(TC_3.A.1.1.3) master:MattC
49  ABC_transporter_heme_(TC3.A.1.107.1)    MattC  ABC_transporter_heme_(TC3.A.1.107.1)    master:MattC
50  ABC_transporter_histidine_lysine_arginine_ornithine_(TC_3.A.1.3.1)      MattC  ABC_transporter_histidine_lysine_arginine_ornithine_(TC_3.A.1.3.1)      master:MattC
51  ABC_transporter_iron(III)_dicitrate_(TC_3.A.1.14.1)     MattC  ABC_transporter_iron(III)_dicitrate_(TC_3.A.1.14.1)     master:MattC
52  ABC_transporter_macrolide       MattC  ABC_transporter_L-proline_glycine_betaine_(TC_3.A.1.12.1)       master:MattC
53  ABC_transporter_maltose MattC  ABC_transporter_macrolide       master:MattC
54  ABC_transporter_molybdenum_(TC_3.A.1.8.1)       MattC  ABC_transporter_maltose master:MattC
55  ABC_transporter_nickel_(TC_3.A.1.5.3)   MattC  ABC_transporter_molybdenum_(TC_3.A.1.8.1)       master:MattC
56  ABC_transporter_oligopeptide_(TC_3.A.1.5.1)     MattC  ABC_transporter_nickel_(TC_3.A.1.5.3)   master:MattC
57  ABC_transporter_peptide_(TC_3.A.1.5.5)  MattC  ABC_transporter_oligopeptide_(TC_3.A.1.5.1)     master:MattC
58  ABC_transporter_phosphate_(TC_3.A.1.7.1)        MattC  ABC_transporter_peptide_(TC_3.A.1.5.5)  master:MattC
59  ABC_transporter_polyamine_putrescine_spermidine_(TC_3.A.1.11.1) MattC  ABC_transporter_phosphate_(TC_3.A.1.7.1)        master:MattC
60  ABC_transporter_putrescine_(TC_3.A.1.11.2)      MattC  ABC_transporter_polyamine_putrescine_spermidine_(TC_3.A.1.11.1) master:MattC
61  ABC_transporter_ribose_(TC_3.A.1.2.1)   MattC  ABC_transporter_putrescine_(TC_3.A.1.11.2)      master:MattC
62  Adhesion_to_eukaryotic_cell     MikeK  ABC_transporter_ribose_(TC_3.A.1.2.1)   master:MattC
63  Alanine_Biosynthesis    Straw  ABC_transporter_tungstate_(TC_3.A.1.6.2)        master:gjo
64  Allantoin_degradation   MattC  Accessory_Gene_Regulator        master:jcassat
65  Ammonia_assimilation    EdF  Acetogenesis_from_Pyruvate      master:LienC_UCSD
66  Anaerobic_respiratory_reductases        OlgaV  Alanine_Biosynthesis    master:Straw
67    Alkaloid_biosynthesis_from_L-lysine     master:OlgaV
68    Alkaloid_biosynthesis_from_putrescine   master:OlgaV
69    Alkaloid_biosynthesis_from_tyrosine     master:OlgaV
70    Alkanesulfonate_assimilation    master:OlgaV
71    Alkanesulfonates_Utilization    master:RobE
72    Allantoin_degradation   master:MattC
73    Ammonia_assimilation    master:EdF
74    Anaerobic_benzoate_metabolism   master:MatthewH_UFL
75    Anaerobic_respiratory_reductases        master:OlgaV
76    Anthocyanin_biosynthesis        master:OlgaV
77    Anthracycline_biosynthesis      master:OlgaV
78    Apigenin_derivatives    master:OlgaV
79    Archaeal_Flagellum      master:RickS
80  Arginine_Biosynthesis   RickS  Arginine_Biosynthesis   RickS
81  Arginine_Putrescine_and_4-aminobutyrate_degradation     MattC  Arginine_Putrescine_and_4-aminobutyrate_degradation     master:MattC
82  Asp-Glu-tRNA(Asn-Gln)_transamidation    gjo  Aromatic_Amin_Catabolism        master:OlgaV
83  Bacterial_Cell_Division RickS  Aromatic_amino_acid_degradation master:OlgaV
84  Betaine_biosynthesis    MattC  Asp-Glu-tRNA(Asn-Gln)_transamidation    master:gjo
85  Bilin_Biosynthesis      OlgaZ  Auxin_biosynthesis      master:OlgaV
86  Biotin_biosynthesis     rodionov  Auxin_degradation       master:OlgaV
87  Branched-Chain_Amino_Acid_Biosynthesis  RossO  Bacterial_Apoptosis     master:KaitlynH
88  CMP-N-acetylneuraminate_Biosynthesis    OlgaZ  Bacterial_Cell_Division master:RickS
89  Calvin-Benson_cycle     SvetaG  Bacterial_Chemotaxis    master:RickS
90  Carotenoids     OlgaV  Bacterial_motility:Gliding      master:OlgaV
91  Chlorophyll_Biosynthesis        VeronikaV  Benzoate_catabolism     master:changhaobi-ufl
92  Chorismate_Synthesis    VeronikaV  Benzoate_degradation    master:OlgaV
93  Coenzyme_A_Biosynthesis AndreiO  Betaine_biosynthesis    master:MattC
94  Cyanobacterial_CO2_uptake       OlgaV  Biflavanoid_biosynthesis        master:OlgaV
95  Cyanobacterial_Circadian_Clock  OlgaZ  Bilin_Biosynthesis      master:OlgaZ
96  Cyanophycin_metabolism  MikeR  Biotin_biosynthesis     master:rodionov
97  Cytochrome_B6-F_complex SvetaG  Biphenyl_Degradation    master:OlgaV
98  Cytolethal_distending_toxin_of_Campylobacter_jejuni     OlgaZ  Bis-_and_Tris-Indole_alkaloids  master:OlgaV
99  D-arabinose_degradation MattC  Branched-Chain_Amino_Acid_Biosynthesis  master:RossO
100  D-galactarate_degradation       MattC  Bsub-Spore-Coat master:RickS
101  D-galacturonate_degradation     MattC  Butyrate_and_Butanol_Acetone_fermentation       master:SouravB_UCSD
102  DNA-replication RickS  Caffeic_acid_derivatives        master:OlgaV
103  DNA_Repair_Base_Excision        MikeK  Calvin-Benson_cycle     master:SvetaG
104  De_Novo_Purine_Biosynthesis     RossO  Cannabinoid_biosynthesis        master:OlgaV
105  De_Novo_Pyrimidine_Synthesis    RossO  Capsular_heptose_biosynthesis   master:OlgaZ
106  Denitrification rodionov  Capsular_polysaccharide_biosynthesis_in_Staphylococcus  master:JenZ
107  Embden-Meyerhof_and_Gluconeogenesis     SvetaG  Capsular_surface_virulence_antigen_loci master:JenZ
108  F0F1-type_ATP_synthase  RickS  Carbon_monoxide_dehydrogenases  master:rodionov
109  FMN_and_FAD_biosynthesis        AndreiO  Carboxysome     master:MalgorzataG_UFL
110  Fatty_Acid_Biosynthesis_FASII   AndreiO  carnitine_metabolism    master:MattC
111  Fe-S_cluster_assembly   rodionov  Carotenoids     master:OlgaV
112  Flagellum       RickS  Catechol_branch_of_beta-ketoadipate_pathway     master:OlgaV
113  Folate_Biosynthesis     vcrecy  CbiQO-type_ABC_transporter_systems      master:rodionov
114  Fucose_and_rhamnose_degradation MattC  Central_meta-cleavage_pathway_of_aromatic_compound_degradation  master:OlgaV
115  Galactitol_degradation  MattC  Chloroaromatic_degradation_pathway      master:OlgaV
116  Galactose_degradation   MattC  Chlorophyll_Biosynthesis        master:VeronikaV
117  General_secretory_pathway_(Sec-SRP)_complex_(TC_3.A.5.1.1)      MattC  Chlorophyll_Degradation master:SvetaG
118  Glutamate,_aspartate_and_asparagine_biosynthisis        MattC  Cholera_toxin   master:VeronikaV
119  Glutamate_biosynthesis  MattC  Choline_Transport       master:RobE
120  Glutathione_Redox_Metabolism    Neema_UCSD  Chorismate_Synthesis    master:VeronikaV
121  Glycerol_Metabolism     MattC  Citrate_Metabolism,_Transport,_and_Regulation   master:JenZ
122  Glycerolipid_and_glycerphospholipid_metabolism  VasiliyP  Clavulanic_acid_biosynthesis    master:OlgaV
123  Glycine_synthesis       MikeK  CMP-N-acetylneuraminate_Biosynthesis    master:OlgaZ
124  Glyoxylate_Synthesis    RickS  Cobalamin_synthesis     master:gjo
125  GroEL_GroES     MikeK  Coenzyme_A_Biosynthesis master:AndreiO
126  HMG_CoA_Synthesis       Veronika  Coenzyme_A_Biosynthesis_in_Pathogens    master:AndreiO
127  Hexitol_degradation     MattC  Coenzyme_F420-H2_dehydrogenase_(methanophenazine)       master:gjo
128  Histidine_Biosynthesis  RossO  Coenzyme_F420_hydrogenase       master:gjo
129  Histidine_Degradation   RossO  Coenzyme_F420_synthesis master:gjo
130  Inorganic_Sulfur_Assimilation   ChristianR  coenzyme_M_biosynthesis master:AdamF
131  Inositol_catabolism     VeronikaV  Coenzyme_PQQ_synthesis  master:gjo
132  Isoprenoid_Biosynthesis OlgaZ  Colanic_acid_biosynthesis       master:JenZ
133  Ketogluconate_metabolism        MattC  Coumarin_biosynthesis   master:OlgaV
134  L-ascorbate_degradation MattC  Cyanobacterial_Circadian_Clock  master:OlgaZ
135  Lactose_degradation     MattC  Cyanobacterial_CO2_uptake       master:OlgaV
136  Leucine_Degradation_and_HMG-CoA_Metabolism      VeronikaV  Cyanophycin_metabolism  master:MikeR
137  Lysine_Biosynthesis_DAP_Pathway AndreiO  cysteine_biosynthesis   master:RobE
138  Mannose-sensitive_hemagglutinin_type_4_pilus    RobE  Cytochrome_B6-F_complex master:Sveta
139  Mannose_and_fructose_metabolism HanYuC_UCSD  Cytochrome_oxidase_assembly_factors     master:SvetaG
140  Menaquinone_and_Phylloquinone_Biosynthesis      OlgaZ  Cytolethal_distending_toxin_of_Campylobacter_jejuni     master:OlgaZ
141  Methanogenesis  gjo  Cytoskeleton    master:JenZ
142  Methionine_Biosynthesis rodionov  Cytotoxic_Polyacetylenes        master:OlgaV
143  Methylcitrate_cycle     MattC  D-alanyl_lipoteichoic_acid_Biosynthesis master:OlgaZ
144  N-Acetyl-D-Glucosamine_Utilization      OlgaZ  D-arabinose_degradation master:MattC
145  N-linked_Glycosylation_in_Bacteria      OlgaZ  D-galactarate_degradation       master:MattC
146  NAD_and_NADP_cofactor_biosynthesis_global       AndreiO  D-galacturonate_degradation     master:MattC
147  Na(+)-translocating_NADH-quinone_oxidoreductase_and_rnf-like_group_of_electron_transport_complexes      OlgaV  D-glucarate_degradation master:MattC
148  Nitrate_and_nitrite_ammonification      rodionov  D-tyrosyl-tRNA(Tyr)_deacylase   master:gjo
149  Nitrosative_stress      rodionov  De_Novo_Purine_Biosynthesis     master:RossO
150  P-type_ATPase_transporter_potassium_(TC_3.A.3.7.1)      MattC  De_Novo_Pyrimidine_Synthesis    master:RossO
151  Pentose_phosphate_pathway       SvetaG  Dehydrogenase_complexes master:VeronikaV
152  Peptidoglycan_Biosynthesis      RickS  Denitrification master:rodionov
153  Phenylalanine_synthesis MikeK  Differentiation_in_bacteria:transcription_factors_and_signaling_systems master:OlgaV
154  Photosystem_I   SvetaG  DNA-replication master:RickS
155  Photosystem_II  SvetaG  DNA_repair,_bacterial   master:gjo
156  Phycobilisome   OlgaZ  DNA_repair_and_recombination_eukaryotic master:gjo
157  Plastoquinone_Biosynthesis      OlgaZ  DNA_Repair_Base_Excision        master:MikeK
158  Polyamine_Metabolism    InesT_UCSD  dTDP-rhamnose_synthesis master:MikeK
159  Porphyrin,_Heme,_and_Siroheme_Biosynthesis      SvetaG  Embden-Meyerhof_and_Gluconeogenesis     master:SvetaG
160  Proline_Synthesis       RickS  Embden-Meyerhof_and_Gluconeogenesis_Archaeal    master:SvetaG
161  Proteasome_archaeal     gjo  Entner-Doudoroff_Pathway        master:SvetaG
162  Proteasome_eukaryotic   gjo  Ethanolamine_utilization        master:gjo
163  Pterin_biosynthesis     vcrecy  F0F1-type_ATP_synthase  master:RickS
164  Purine_conversions      OlgaV  Fatty_Acid_Biosynthesis_FASII   master:AndreiO
165  Pyruvate_Alanine_Serine_Interconversions        JasonS_UCSD  fatty_acid_metabolism   master:MattC
166  Queuosine-Archaeosine_Biosynthesis      vcrecy  fatty_acid_oxidation_pathway    master:MattC
167  RNA_polymerase_I        gjo  Fe-S_cluster_assembly   master:rodionov
168  RNA_polymerase_II       gjo  Fermentations:_Lactate  master:SvetaG
169  RNA_polymerase_III      gjo  Fermentations:_Mixed_acid       master:SvetaG
170  RNA_polymerase_II_initiation_factors    gjo  Flagellum       master:RickS
171  RNA_polymerase_archaeal gjo  Flavanone_biosynthesis  master:OlgaV
172  RNA_polymerase_archaeal_initiation_factors      gjo  FMN_and_FAD_biosynthesis        master:AndreiO
173  RNA_polymerase_bacterial        gjo  FMN_and_FAD_biosynthesis_in_pathogens   master:AndreiO
174  RNA_polymerase_chloroplast      gjo  Folate_Biosynthesis     master:vcrecy
175  Resistance_to_fluoroquinolones  MattC  Formate_dehydrogenase   master:gjo
176  Respiratory_Complex_I   OlgaV  Formate_hydrogenase     master:OlgaV
177  Respiratory_dehydrogenases_1    OlgaV  Fructose-bisphosphate_aldolase_protein_family   master:SvetaG
178  Ribonucleotide_reduction        rodionov  Fucose_and_rhamnose_degradation master:MattC
179  Ribose_and_deoxyribose_phosphate_metabolism     MattC  Fungal_cytostatics      master:OlgaV
180  Ribosome_LSU_bacterial  gjo  Fungal_differentiation_factors  master:OlgaV
181  Ribosome_LSU_eukaryotic_and_archaeal    gjo  Galactitol_degradation  master:MattC
182  Ribosome_SSU_bacterial  gjo  Galactose_degradation   master:MattC
183  Ribosome_SSU_chloroplast        gjo  General_secretory_pathway_(Sec-SRP)_complex_(TC_3.A.5.1.1)      master:MattC
184  Ribosome_SSU_eukaryotic_and_archaeal    gjo  Glutamate,_aspartate_and_asparagine_biosynthesis        master:MattC
185  Ribosome_biogenesis_bacterial   gjo  Glutamate_biosynthesis  master:MattC
186  Serine_Biosynthesis     MikeK  Glutamyl_peptidase?     master:RamyA
187  Siderophore_Aerobactin_and_Ferrichrome_Biosynthesis     MattC  Glutathione_Redox_Metabolism    master:Neema_UCSD
188  Soluble_cytochromes_and_functionally_related_electron_carriers  OlgaV  Glycerol_fermenation_to_1,3-propanediol master:gjo
189  Succinate_dehydrogenase OlgaV  Glycerol_Metabolism     master:MattC
190  Sulfate_assimilation    MattC  Glycerolipid_and_glycerphospholipid_metabolism  master:VasiliyP_UCSD
191  Sulfur_Metabolism       RobE  Glycine_cleavage_system master:MattC
192  TCA_Cycle       OlgaV  Glycine_reductase,_sarcosine_reductase_and_betaine_reductase    master:gjo
193  Terminal_cytochrome_C_oxidases  OlgaV  Glycine_synthesis       master:MikeK
194  Terminal_cytochrome_oxidases    OlgaV  glyoxylate_degradation  master:MattC
195  Thiamin_biosynthesis    rodionov  Glyoxylate_Synthesis    master:RickS
196  Threonine_synthesis     MikeK  Gram-Positive_Extracellular_Nucleases   master:RamyA
197  Tocopherol_Biosynthesis OlgaZ  gram_plus_late_competence       master:alexS
198  Transcription_factors_bacterial gjo  GroEL_GroES     master:MikeK
199  Translation_elongation_factors_eukaryotic_and_archaeal  gjo  Heavy_metal_ion_sensors_and_exporters   master:JenZ
200  Translation_factors_bacterial   gjo  Heme-bound_Iron_Scavenge_Pathway        master:RickS
201  Translation_initiation_factors_eukaryotic_and_archaeal  gjo  Hexitol_degradation     master:MattC
202  Transport_of_Nickel_and_Cobalt  rodionov  Histidine_Biosynthesis  master:RossO
203  Trehalose_biosynthesis  MattC  Histidine_Degradation   master:RossO
204  Tricarballylate_Utilization     RossO  HMG_CoA_Synthesis       master:VeronikaV
205  Tryptophan_synthesis    VeronikaV  Homogentisate_pathway_of_aromatic_compound_degradation  master:OlgaV
206  Tyrosine_synthesis      MikeK  hpa_catabolic_pathway   master:YakovK
207  UDP-N-acetylmuramate_from_Fructose-6-phosphate_Biosynthesis     VasiliyP  Hydrogenases    master:OlgaV
208  Ubiquinone_Biosynthesis OlgaZ  Inorganic_Sulfur_Assimilation   master:ChristianR
209  Ubiquinone_Menaquinone-cytochrome_c_reductase_complexes OlgaV  Inositol_catabolism     master:VeronikaV
210  Urea_decomposition      rodionov  Intercellular_adhesion_SA       master:MattC
211  V-Type_ATP_synthase     RickS  Isoleucine_degradation  master:OlgaZ
212  carnitine_metabolism    MattC  Isoprenoid_Biosynthesis master:OlgaZ
213  cysteine_biosynthesis   RobE  KDO2-Lipid_A_biosynthesis       master:OlgaZ
214  dTDP-rhamnose_synthesis MikeK  Ketogluconate_metabolism        master:MattC
215  fatty_acid_metabolism   MattC  L-ascorbate_degradation master:MattC
216  fatty_acid_oxidation_pathway    MattC  Lactose_degradation     master:MattC
217  glyoxylate_degradation  MattC  Leucine_Biosynthesis_v2 master:AdamF
218  mannose_and_GDP-mannose_metabolism      MattC  Leucine_Degradation_and_HMG-CoA_Metabolism      master:VeronikaV
219  polyisoprenoid_biosynthesis     MattC  Lignine_biosynthesis    master:OlgaV
220  ppGpp_biosynthesis      MikeK  linker_unit-arabinogalactan_synthesis   master:NJ
221  tRNA_aminoacylation     gjo  Lipid_A_biosynthesis    master:OlgaZ
222  tRNA_processing gjo  Lipid_A_modifications   master:OlgaZ
223  tRNA_splicing   gjo  Lipoic_acid_metabolism  master:gjo
224    Lipoteichoic_acid_biosynthesis  master:RamyA
225    Listeria_Pathogenicity_Island_LIPI-1_extended   master:SvetaG
226    Listeria_surface_proteins:_Internalin-like_proteins     master:SvetaG
227    Listeria_surface_proteins:_LPXTG_motif  master:SvetaG
228    LMPTP_YfkJ_cluster      master:AndreiO
229    LMPTP_YwlE_cluster      master:AndreiO
230    LOS_core_oligosaccharide_biosynthesis   master:OlgaZ
231    Lysine_Biosynthesis_DAP_Pathway master:AndreiO
232    Malonate_decarboxylase  master:VeronikaV
233    Mannose-sensitive_hemagglutinin_type_4_pilus    master:RobE
234    Mannose_and_fructose_metabolism master:HanYuC_UCSD
235    mannose_and_GDP-mannose_metabolism      master:MattC
236    Membrane-bound_Ni,_Fe-hydrogenase       master:rodionov
237    Menaquinone_and_Phylloquinone_Biosynthesis      master:OlgaZ
238    Menaquinone_Biosynthesis        master:RickS
239    Mercury_resistance_operon       master:JenZ
240    Methane_metabolism      master:MikeR
241    Methanogenesis  master:gjo
242    Methanogenesis_from_methylated_compounds        master:gjo
243    Methanophenazine_hydrogenase    master:gjo
244    methanopterin_biosynthesis      master:AdamF
245    Methionine_Biosynthesis master:rodionov
246    Methionine_Salvage      master:gjo
247    Methylcitrate_cycle     master:MattC
248    Methylglyoxal_Metabolism        master:OlgaZ
249    MLST    master:RobE
250    Molybdopterin_biosynthesis      master:JenZ
251    mycolic_acid_synthesis  master:NJ
252    N-Acetyl-D-Glucosamine_Utilization      master:OlgaZ
253    N-heterocyclic_aromatic_compound_degradation    master:OlgaV
254    N-linked_Glycosylation_in_Bacteria      master:OlgaZ
255    n-Phenylalkanoic_acid_degradation       master:OlgaV
256    Na(+)-translocating_NADH-quinone_oxidoreductase_and_rnf-like_group_of_electron_transport_complexes      master:OlgaV
257    NAD_and_NADP_cofactor_biosynthesis_global       master:AndreiO
258    NAD_and_NADP_cofactor_biosynthesis_in_pathogens master:AndreiO
259    NAD_and_NADP_paper      master:SvetaG
260    NAD_and_NADP_tutorial_10        master:AndreiO
261    Naphtalene_and_antracene_degradation    master:OlgaV
262    NiFe_hydrogenase_maturation     master:gjo
263    Nitrate_and_nitrite_ammonification      master:rodionov
264    Nitrosative_stress      master:rodionov
265    NusA-TFII_Cluster       master:gjo
266    O-linked_flagella_Glycosylation master:OlgaZ
267    Octadecanoids   master:OlgaV
268    Osmotically_activated_L-carnitine_ABC_transporter_in_Listeria   master:JenZ
269    Oxidative_stress        master:OlgaV
270    Oxidative_stress_(animal_systems)       master:OlgaV
271    Oxidative_stress_in_bacteria    master:OlgaV
272    p-Hydroxybenzoate_degradation   master:OlgaV
273    P-type_ATPase_transporter_potassium_(TC_3.A.3.7.1)      master:MattC
274    P_uptake_(cyanobacteria)        master:acm_at_mit
275    Pentose_phosphate_pathway       master:SvetaG
276    Peptidoglycan_Biosynthesis      master:RickS
277    Phenylacetate_pathway_of_aromatic_compound_degradation  master:OlgaV
278    Phenylalanine_synthesis master:MikeK
279    Phenylpropanoid_compound_degradation    master:OlgaV
280    Phenylpropanoids_general_biosynthesis   master:OlgaV
281    Phenylpropionate_Degradation    master:OlgaV
282    Phosphoglycerate_mutase_protein_family  master:SvetaG
283    Phosphotransferase_enzyme_II_-_Glucose_class_permease   master:JenZ
284    Phosphotransferase_enzyme_II_-_Lactose_class_permease   master:JenZ
285    Phosphotransferase_enzyme_II_-_Mannitol_class_permease  master:JenZ
286    Phosphotransferase_enzyme_II_-_Mannose_family_permease  master:JenZ
287    Photosystem_I   master:SvetaG
288    Photosystem_II  master:SvetaG
289    Phycobilisome   master:OlgaZ
290    Phytoalexin_biosynthesis        master:OlgaV
291    Phytochromes    master:OlgaZ
292    Phytosterol_biosynthesis        master:OlgaV
293    Plastoquinone_Biosynthesis      master:OlgaZ
294    Polyadenylation_bacterial       master:gjo
295    Polyamine_Metabolism    master:InesT_UCSD
296    polyisoprenoid_biosynthesis     master:MattC
297    polyprenyl_synthesis    master:NJ
298    Porphyrin,_Heme,_and_Siroheme_Biosynthesis      master:SvetaG
299    ppGpp_biosynthesis      master:MikeK
300    Proline_Catabolism      master:laszloC
301    Proline_degradation     master:unknown
302    Proline_degradation1    master:unknown
303    Proline_Synthesis       master:RickS
304    Propanediol_utilization master:gjo
305    Prophage-encoded_Exotoxins      master:RamyA
306    Prophage_lysogenic_conversion_modules   master:RamyA
307    Proteasome_archaeal     master:gjo
308    Proteasome_eukaryotic   master:gjo
309    Protection_from_Reactive_Oxygen_Species master:MikeK
310    Protein_Acetylation_and_Deacetylation_in_Bacteria       master:AndreiO
311    Protein_degradation     master:gjo
312    Proteolysis_in_bacteria,_ATP-dependent  master:OlgaZ
313    Protocatechuate_branch_of_beta-ketoadipate_pathway      master:OlgaV
314    Protozoan_cytostatics_and_differentiation_factors       master:OlgaV
315    Pterin_biosynthesis     master:vcrecy
316    Purine_conversions      master:OlgaV
317    pyrimidine_conversions  master:RossO
318    Pyrroloquinoline_Quinone_biosynthesis   master:OlgaZ
319    Pyruvate:ferredoxin_oxidoreductase      master:SvetaG
320    Pyruvate_Alanine_Serine_Interconversions        master:JasonS_UCSD
321    Pyruvate_metabolism_I:_anaplerotic_reactions,_PEP       master:SvetaG
322    Queuosine-Archaeosine_Biosynthesis      master:vcrecy
323    Quinate_degradation     master:OlgaV
324    Quinolinic_acid_and_its_derivatives     master:OlgaV
325    Quorum_Sensing:_Autoinducer-2_Synthesis master:AndrewJ
326    Redox-dependent_regulation_of_nucleus_processes master:OlgaV
327    Resistance_to_fluoroquinolones  master:MattC
328    Resistance_to_Vancomycin        master:MattC
329    Respiratory_Complex_I   master:OlgaV
330    Respiratory_dehydrogenases_1    master:OlgaV
331    Riboflavin_metabolism   master:rodionov
332    Ribonuclease_P_archaeal_and_eukaryal    master:gjo
333    Ribonucleotide_reduction        master:rodionov
334    Ribose_and_deoxyribose_phosphate_metabolism     master:MattC
335    Ribosome_biogenesis_bacterial   master:gjo
336    Ribosome_LSU_bacterial  master:gjo
337    Ribosome_LSU_chloroplast        master:gjo
338    Ribosome_LSU_eukaryotic_and_archaeal    master:gjo
339    Ribosome_LSU_mitochondrial      master:gjo
340    Ribosome_SSU_bacterial  master:gjo
341    Ribosome_SSU_chloroplast        master:gjo
342    Ribosome_SSU_eukaryotic_and_archaeal    master:gjo
343    Ribosome_SSU_mitochondrial      master:gjo
344    RNA_polymerase_archaeal master:gjo
345    RNA_polymerase_archaeal_initiation_factors      master:gjo
346    RNA_polymerase_bacterial        master:gjo
347    RNA_polymerase_chloroplast      master:gjo
348    RNA_polymerase_I        master:gjo
349    RNA_polymerase_II       master:gjo
350    RNA_polymerase_II_initiation_factors    master:gjo
351    RNA_polymerase_III      master:gjo
352    Rrf2_family_transcriptional_regulators  master:rodionov
353    Salicylate_ester_degradation    master:OlgaV
354    Salicylic_acid_biosynthesis1    master:OlgaV
355    Selenocysteine_metabolism       master:gjo
356    Serine_Biosynthesis     master:MikeK
357    Siderophore_Aerobactin_and_Ferrichrome_Biosynthesis     master:MikeK
358    Siderophore_enterobactin_biosynthesis   master:MattC
359    Siderophore_enterobactin_biosynthesis_and_ferric_enterbactin_transport  master:MattC
360    Siderophore_Yersiniabactin_Biosynthesis master:MikeK
361    SLO-NADGH_Locus master:RamyA
362    Sodium_Hydrogen_Antiporter      master:JenZ
363    Soluble_cytochromes_and_functionally_related_electron_carriers  master:OlgaV
364    SpeB-SpeF_extended_regulon      master:RamyA
365    Sphingolipid_biosynthesis       master:JorgeF
366    Spliceosome     master:gjo
367    Spore_Coat      master:RickS
368    Steroid_sulfates        master:OlgaV
369    Streptococcal_Hyaluronic_Acid_Capsule   master:RamyA
370    Streptococcal_Mga_Regulon       master:RamyA
371    Streptococcus_pyogenes_Transcription_Regulators master:RamyA
372    Streptococcus_pyogenes_Virulome master:RamyA
373    Streptolysin_S_Biosynthesis_and_Transport       master:RamyA
374    Streptomycin_biosynthesis       master:OlgaV
375    Suberine_biosynthesis   master:OlgaV
376    Succinate_dehydrogenase master:OlgaV
377    Sucrose_Metabolism      master:MattC
378    Sulfate_assimilation    master:MattC
379    Sulfate_to_Sulfide      master:RobE
380    Sulfur_Metabolism       master:RobE
381    Tannin_biosynthesis     master:OlgaV
382    Taurine_Utilization     master:RobE
383    TCA_Cycle       master:OlgaV
384    Teichoic_acid_Biosynthesis      master:OlgaZ
385    Terminal_cytochrome_C_oxidases  master:OlgaV
386    Terminal_cytochrome_oxidases    master:OlgaV
387    Terpen_biosynthesis     master:OlgaV
388    The_Tartronate_Semialdehyde_Hub master:RossO
389    Thiamin_biosynthesis    master:rodionov
390    Thioredoxin-disulfide_reductase master:gjo
391    Threonine_degradation   master:OlgaV
392    Threonine_synthesis     master:MikeK
393    Tocopherol_Biosynthesis master:OlgaZ
394    Toluene_degradation     master:OlgaV
395    Transcription_factors_bacterial master:gjo
396    Transcription_factors_cyanobacterial_RpoD-like_sigma_factors    master:gjo
397    Translation_elongation_factors_eukaryotic_and_archaeal  master:gjo
398    Translation_factors_bacterial   master:gjo
399    Translation_initiation_factors_eukaryotic_and_archaeal  master:gjo
400    Transport_of_Nickel_and_Cobalt  master:rodionov
401    Trehalose_biosynthesis  master:MattC
402    Triacylglycerol_biosynthesis    master:unknown
403    Triacylglycerol_degradation     master:unknown
404    Tricarballylate_Utilization     master:RossO
405    tRNA_aminoacylation     master:gjo
406    tRNA_aminoacylation,_mitochondrial      master:gjo
407    tRNA_processing master:gjo
408    tRNA_splicing   master:gjo
409    Tryptophan_synthesis    master:VeronikaV
410    Tyrosine_synthesis      master:MikeK
411    Ubiquinone_Biosynthesis master:OlgaZ
412    Ubiquinone_Menaquinone-cytochrome_c_reductase_complexes master:OlgaV
413    UDP-N-acetylmuramate_from_Fructose-6-phosphate_Biosynthesis     master:vasiliyP
414    Universal_GTPases       master:gjo
415    Urea_decomposition      master:rodionov
416    Utilization_of_glutathione_as_a_sulphur_source  master:OlgaV
417    V-Type_ATP_synthase     master:RickS
418    Valine_Biosynthesis     master:Straw
419    Valine_degradation      master:OlgaZ
420    Vibrio_Experimental_Type_III_secretion_system   master:JanelleT
421  //  //
422  END  END
423  ;  ;
424      return split(/\n/,$x);      return split(/\n/,$x);
425  }  }
426    
427    
428  sub choose_best_assignment {  sub choose_best_assignment {
429      my($fig,$parms,$pegs,$external_ids) = @_;      my($fig,$parms,$pegs,$external_ids) = @_;
430      my($peg,$id);      my($peg,$id);
# Line 307  Line 518 
518              my $incr = @$x;              my $incr = @$x;
519              foreach $_ (@$x)              foreach $_ (@$x)
520              {              {
521                  if (((100 * $_->[0]) + $incr) > $best_score)                  my($sc,$peg,$in_sub) = @$_;
522                    $sc += $in_sub ? 10000 : 0;
523    
524                    if (((100 * $sc) + $incr) > $best_score)
525                  {                  {
526                      $best_score = (100 * $_->[0]) + $incr;                      $best_score = (100 * $sc) + $incr;
527                      $best_func  = $func;                      $best_func  = $func;
528                      $best_source = $_->[1];                      $best_source = $peg;
529                  }                  }
530              }              }
531          }          }
# Line 348  Line 562 
562          my $subv = 0;          my $subv = 0;
563          my @subs = $fig->peg_to_subsystems($peg);          my @subs = $fig->peg_to_subsystems($peg);
564          my $sub;          my $sub;
565            my $in_sub = 0;
566          foreach $sub (@subs)          foreach $sub (@subs)
567          {          {
568              if (($_ = $parms->{'subsystems'}->{$sub}) && ($_ > $subv))              if ($_ = $parms->{'subsystems'}->{$sub})
569                {
570                    if ($_ > $subv)
571              {              {
572                  $subv = $_;                  $subv = $_;
573              }              }
574                    $in_sub = 1;
575                }
576          }          }
577          $value += $subv;          $value += $subv;
578            push(@{$functions->{$func}},[$value,$peg,$in_sub]);
         push(@{$functions->{$func}},[$value,$peg]);  
579      }      }
580  }  }
581    

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