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revision 1.2, Sun Aug 14 01:47:51 2005 UTC revision 1.6, Thu Dec 22 00:52:43 2005 UTC
# Line 1  Line 1 
1    #
2    # Copyright (c) 2003-2006 University of Chicago and Fellowship
3    # for Interpretations of Genomes. All Rights Reserved.
4    #
5    # This file is part of the SEED Toolkit.
6    #
7    # The SEED Toolkit is free software. You can redistribute
8    # it and/or modify it under the terms of the SEED Toolkit
9    # Public License.
10    #
11    # You should have received a copy of the SEED Toolkit Public License
12    # along with this program; if not write to the University of Chicago
13    # at info@ci.uchicago.edu or the Fellowship for Interpretation of
14    # Genomes at veronika@thefig.info or download a copy from
15    # http://www.theseed.org/LICENSE.TXT.
16    #
17    
18  package Assignments;  package Assignments;
19    
20  use Carp;  use Carp;
# Line 32  Line 49 
49  genome  192222.1        4       Campylobacter jejuni subsp. jejuni NCTC 11168  genome  192222.1        4       Campylobacter jejuni subsp. jejuni NCTC 11168
50  genome  224308.1        2       Bacillus subtilis subsp. subtilis str. 168  genome  224308.1        2       Bacillus subtilis subsp. subtilis str. 168
51  external        sp      4  external        sp      4
52  external        uni     2  external        uni     1.3
53  external        kegg    1  external        kegg    1
54  subsystems      trusted 8  subsystems      trusted 8
55  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
56  ABC_transporter_alkylphosphonate_(TC_3.A.1.9.1) MattC  ABC_transporter_alkylphosphonate_(TC_3.A.1.9.1) master:MattC
57  ABC_transporter_arabinose_(TC_3.A.1.2.2)        MattC  ABC_transporter_arabinose_(TC_3.A.1.2.2)        master:MattC
58  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
59  ABC_transporter_dipeptide_(TC_3.A.1.5.2)        MattC  ABC_transporter_dipeptide_(TC_3.A.1.5.2)        master:MattC
60  ABC_transporter_ferric_enterobactin_(TC_3.A.1.14.2)     MattC  ABC_transporter_ferric_enterobactin_(TC_3.A.1.14.2)     master:MattC
61  ABC_transporter_ferrichrome_(TC_3.A.1.14.3)     MattC  ABC_transporter_ferrichrome_(TC_3.A.1.14.3)     master:MattC
62  ABC_transporter_galactose_(TC_3.A.1.2.3)        MattC  ABC_transporter_galactose_(TC_3.A.1.2.3)        master:MattC
63  ABC_transporter_glutamate_aspartate_(TC_3.A.1.3.4)      MattC  ABC_transporter_glutamate_aspartate_(TC_3.A.1.3.4)      master:MattC
64  ABC_transporter_glutamine_(TC_3.A.1.3.2)        MattC  ABC_transporter_glutamine_(TC_3.A.1.3.2)        master:MattC
65  ABC_transporter_glycerol_(TC_3.A.1.1.3) MattC  ABC_transporter_glycerol_(TC_3.A.1.1.3) master:MattC
66  ABC_transporter_heme_(TC3.A.1.107.1)    MattC  ABC_transporter_heme_(TC3.A.1.107.1)    master:MattC
67  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
68  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
69  ABC_transporter_macrolide       MattC  ABC_transporter_L-proline_glycine_betaine_(TC_3.A.1.12.1)       master:MattC
70  ABC_transporter_maltose MattC  ABC_transporter_macrolide       master:MattC
71  ABC_transporter_molybdenum_(TC_3.A.1.8.1)       MattC  ABC_transporter_maltose master:MattC
72  ABC_transporter_nickel_(TC_3.A.1.5.3)   MattC  ABC_transporter_molybdenum_(TC_3.A.1.8.1)       master:MattC
73  ABC_transporter_oligopeptide_(TC_3.A.1.5.1)     MattC  ABC_transporter_nickel_(TC_3.A.1.5.3)   master:MattC
74  ABC_transporter_peptide_(TC_3.A.1.5.5)  MattC  ABC_transporter_oligopeptide_(TC_3.A.1.5.1)     master:MattC
75  ABC_transporter_phosphate_(TC_3.A.1.7.1)        MattC  ABC_transporter_peptide_(TC_3.A.1.5.5)  master:MattC
76  ABC_transporter_polyamine_putrescine_spermidine_(TC_3.A.1.11.1) MattC  ABC_transporter_phosphate_(TC_3.A.1.7.1)        master:MattC
77  ABC_transporter_putrescine_(TC_3.A.1.11.2)      MattC  ABC_transporter_polyamine_putrescine_spermidine_(TC_3.A.1.11.1) master:MattC
78  ABC_transporter_ribose_(TC_3.A.1.2.1)   MattC  ABC_transporter_putrescine_(TC_3.A.1.11.2)      master:MattC
79  Adhesion_to_eukaryotic_cell     MikeK  ABC_transporter_ribose_(TC_3.A.1.2.1)   master:MattC
80  Alanine_Biosynthesis    Straw  ABC_transporter_tungstate_(TC_3.A.1.6.2)        master:gjo
81  Allantoin_degradation   MattC  Accessory_Gene_Regulator        master:jcassat
82  Ammonia_assimilation    EdF  Acetogenesis_from_Pyruvate      master:LienC_UCSD
83  Anaerobic_respiratory_reductases        OlgaV  Alanine_Biosynthesis    master:Straw
84    Alkaloid_biosynthesis_from_L-lysine     master:OlgaV
85    Alkaloid_biosynthesis_from_putrescine   master:OlgaV
86    Alkaloid_biosynthesis_from_tyrosine     master:OlgaV
87    Alkanesulfonate_assimilation    master:OlgaV
88    Alkanesulfonates_Utilization    master:RobE
89    Allantoin_degradation   master:MattC
90    Ammonia_assimilation    master:EdF
91    Anaerobic_benzoate_metabolism   master:MatthewH_UFL
92    Anaerobic_respiratory_reductases        master:OlgaV
93    Anthocyanin_biosynthesis        master:OlgaV
94    Anthracycline_biosynthesis      master:OlgaV
95    Apigenin_derivatives    master:OlgaV
96    Archaeal_Flagellum      master:RickS
97  Arginine_Biosynthesis   RickS  Arginine_Biosynthesis   RickS
98  Arginine_Putrescine_and_4-aminobutyrate_degradation     MattC  Arginine_Putrescine_and_4-aminobutyrate_degradation     master:MattC
99  Asp-Glu-tRNA(Asn-Gln)_transamidation    gjo  Aromatic_Amin_Catabolism        master:OlgaV
100  Bacterial_Cell_Division RickS  Aromatic_amino_acid_degradation master:OlgaV
101  Betaine_biosynthesis    MattC  Asp-Glu-tRNA(Asn-Gln)_transamidation    master:gjo
102  Bilin_Biosynthesis      OlgaZ  Auxin_biosynthesis      master:OlgaV
103  Biotin_biosynthesis     rodionov  Auxin_degradation       master:OlgaV
104  Branched-Chain_Amino_Acid_Biosynthesis  RossO  Bacterial_Apoptosis     master:KaitlynH
105  CMP-N-acetylneuraminate_Biosynthesis    OlgaZ  Bacterial_Cell_Division master:RickS
106  Calvin-Benson_cycle     SvetaG  Bacterial_Chemotaxis    master:RickS
107  Carotenoids     OlgaV  Bacterial_motility:Gliding      master:OlgaV
108  Chlorophyll_Biosynthesis        VeronikaV  Benzoate_catabolism     master:changhaobi-ufl
109  Chorismate_Synthesis    VeronikaV  Benzoate_degradation    master:OlgaV
110  Coenzyme_A_Biosynthesis AndreiO  Betaine_biosynthesis    master:MattC
111  Cyanobacterial_CO2_uptake       OlgaV  Biflavanoid_biosynthesis        master:OlgaV
112  Cyanobacterial_Circadian_Clock  OlgaZ  Bilin_Biosynthesis      master:OlgaZ
113  Cyanophycin_metabolism  MikeR  Biotin_biosynthesis     master:rodionov
114  Cytochrome_B6-F_complex SvetaG  Biphenyl_Degradation    master:OlgaV
115  Cytolethal_distending_toxin_of_Campylobacter_jejuni     OlgaZ  Bis-_and_Tris-Indole_alkaloids  master:OlgaV
116  D-arabinose_degradation MattC  Branched-Chain_Amino_Acid_Biosynthesis  master:RossO
117  D-galactarate_degradation       MattC  Bsub-Spore-Coat master:RickS
118  D-galacturonate_degradation     MattC  Butyrate_and_Butanol_Acetone_fermentation       master:SouravB_UCSD
119  DNA-replication RickS  Caffeic_acid_derivatives        master:OlgaV
120  DNA_Repair_Base_Excision        MikeK  Calvin-Benson_cycle     master:SvetaG
121  De_Novo_Purine_Biosynthesis     RossO  Cannabinoid_biosynthesis        master:OlgaV
122  De_Novo_Pyrimidine_Synthesis    RossO  Capsular_heptose_biosynthesis   master:OlgaZ
123  Denitrification rodionov  Capsular_polysaccharide_biosynthesis_in_Staphylococcus  master:JenZ
124  Embden-Meyerhof_and_Gluconeogenesis     SvetaG  Capsular_surface_virulence_antigen_loci master:JenZ
125  F0F1-type_ATP_synthase  RickS  Carbon_monoxide_dehydrogenases  master:rodionov
126  FMN_and_FAD_biosynthesis        AndreiO  Carboxysome     master:MalgorzataG_UFL
127  Fatty_Acid_Biosynthesis_FASII   AndreiO  carnitine_metabolism    master:MattC
128  Fe-S_cluster_assembly   rodionov  Carotenoids     master:OlgaV
129  Flagellum       RickS  Catechol_branch_of_beta-ketoadipate_pathway     master:OlgaV
130  Folate_Biosynthesis     vcrecy  CbiQO-type_ABC_transporter_systems      master:rodionov
131  Fucose_and_rhamnose_degradation MattC  Central_meta-cleavage_pathway_of_aromatic_compound_degradation  master:OlgaV
132  Galactitol_degradation  MattC  Chloroaromatic_degradation_pathway      master:OlgaV
133  Galactose_degradation   MattC  Chlorophyll_Biosynthesis        master:VeronikaV
134  General_secretory_pathway_(Sec-SRP)_complex_(TC_3.A.5.1.1)      MattC  Chlorophyll_Degradation master:SvetaG
135  Glutamate,_aspartate_and_asparagine_biosynthisis        MattC  Cholera_toxin   master:VeronikaV
136  Glutamate_biosynthesis  MattC  Choline_Transport       master:RobE
137  Glutathione_Redox_Metabolism    Neema_UCSD  Chorismate_Synthesis    master:VeronikaV
138  Glycerol_Metabolism     MattC  Citrate_Metabolism,_Transport,_and_Regulation   master:JenZ
139  Glycerolipid_and_glycerphospholipid_metabolism  VasiliyP  Clavulanic_acid_biosynthesis    master:OlgaV
140  Glycine_synthesis       MikeK  CMP-N-acetylneuraminate_Biosynthesis    master:OlgaZ
141  Glyoxylate_Synthesis    RickS  Cobalamin_synthesis     master:gjo
142  GroEL_GroES     MikeK  Coenzyme_A_Biosynthesis master:AndreiO
143  HMG_CoA_Synthesis       Veronika  Coenzyme_A_Biosynthesis_in_Pathogens    master:AndreiO
144  Hexitol_degradation     MattC  Coenzyme_F420-H2_dehydrogenase_(methanophenazine)       master:gjo
145  Histidine_Biosynthesis  RossO  Coenzyme_F420_hydrogenase       master:gjo
146  Histidine_Degradation   RossO  Coenzyme_F420_synthesis master:gjo
147  Inorganic_Sulfur_Assimilation   ChristianR  coenzyme_M_biosynthesis master:AdamF
148  Inositol_catabolism     VeronikaV  Coenzyme_PQQ_synthesis  master:gjo
149  Isoprenoid_Biosynthesis OlgaZ  Colanic_acid_biosynthesis       master:JenZ
150  Ketogluconate_metabolism        MattC  Coumarin_biosynthesis   master:OlgaV
151  L-ascorbate_degradation MattC  Cyanobacterial_Circadian_Clock  master:OlgaZ
152  Lactose_degradation     MattC  Cyanobacterial_CO2_uptake       master:OlgaV
153  Leucine_Degradation_and_HMG-CoA_Metabolism      VeronikaV  Cyanophycin_metabolism  master:MikeR
154  Lysine_Biosynthesis_DAP_Pathway AndreiO  cysteine_biosynthesis   master:RobE
155  Mannose-sensitive_hemagglutinin_type_4_pilus    RobE  Cytochrome_B6-F_complex master:Sveta
156  Mannose_and_fructose_metabolism HanYuC_UCSD  Cytochrome_oxidase_assembly_factors     master:SvetaG
157  Menaquinone_and_Phylloquinone_Biosynthesis      OlgaZ  Cytolethal_distending_toxin_of_Campylobacter_jejuni     master:OlgaZ
158  Methanogenesis  gjo  Cytoskeleton    master:JenZ
159  Methionine_Biosynthesis rodionov  Cytotoxic_Polyacetylenes        master:OlgaV
160  Methylcitrate_cycle     MattC  D-alanyl_lipoteichoic_acid_Biosynthesis master:OlgaZ
161  N-Acetyl-D-Glucosamine_Utilization      OlgaZ  D-arabinose_degradation master:MattC
162  N-linked_Glycosylation_in_Bacteria      OlgaZ  D-galactarate_degradation       master:MattC
163  NAD_and_NADP_cofactor_biosynthesis_global       AndreiO  D-galacturonate_degradation     master:MattC
164  Na(+)-translocating_NADH-quinone_oxidoreductase_and_rnf-like_group_of_electron_transport_complexes      OlgaV  D-glucarate_degradation master:MattC
165  Nitrate_and_nitrite_ammonification      rodionov  D-tyrosyl-tRNA(Tyr)_deacylase   master:gjo
166  Nitrosative_stress      rodionov  De_Novo_Purine_Biosynthesis     master:RossO
167  P-type_ATPase_transporter_potassium_(TC_3.A.3.7.1)      MattC  De_Novo_Pyrimidine_Synthesis    master:RossO
168  Pentose_phosphate_pathway       SvetaG  Dehydrogenase_complexes master:VeronikaV
169  Peptidoglycan_Biosynthesis      RickS  Denitrification master:rodionov
170  Phenylalanine_synthesis MikeK  Differentiation_in_bacteria:transcription_factors_and_signaling_systems master:OlgaV
171  Photosystem_I   SvetaG  DNA-replication master:RickS
172  Photosystem_II  SvetaG  DNA_repair,_bacterial   master:gjo
173  Phycobilisome   OlgaZ  DNA_repair_and_recombination_eukaryotic master:gjo
174  Plastoquinone_Biosynthesis      OlgaZ  DNA_Repair_Base_Excision        master:MikeK
175  Polyamine_Metabolism    InesT_UCSD  dTDP-rhamnose_synthesis master:MikeK
176  Porphyrin,_Heme,_and_Siroheme_Biosynthesis      SvetaG  Embden-Meyerhof_and_Gluconeogenesis     master:SvetaG
177  Proline_Synthesis       RickS  Embden-Meyerhof_and_Gluconeogenesis_Archaeal    master:SvetaG
178  Proteasome_archaeal     gjo  Entner-Doudoroff_Pathway        master:SvetaG
179  Proteasome_eukaryotic   gjo  Ethanolamine_utilization        master:gjo
180  Pterin_biosynthesis     vcrecy  F0F1-type_ATP_synthase  master:RickS
181  Purine_conversions      OlgaV  Fatty_Acid_Biosynthesis_FASII   master:AndreiO
182  Pyruvate_Alanine_Serine_Interconversions        JasonS_UCSD  fatty_acid_metabolism   master:MattC
183  Queuosine-Archaeosine_Biosynthesis      vcrecy  fatty_acid_oxidation_pathway    master:MattC
184  RNA_polymerase_I        gjo  Fe-S_cluster_assembly   master:rodionov
185  RNA_polymerase_II       gjo  Fermentations:_Lactate  master:SvetaG
186  RNA_polymerase_III      gjo  Fermentations:_Mixed_acid       master:SvetaG
187  RNA_polymerase_II_initiation_factors    gjo  Flagellum       master:RickS
188  RNA_polymerase_archaeal gjo  Flavanone_biosynthesis  master:OlgaV
189  RNA_polymerase_archaeal_initiation_factors      gjo  FMN_and_FAD_biosynthesis        master:AndreiO
190  RNA_polymerase_bacterial        gjo  FMN_and_FAD_biosynthesis_in_pathogens   master:AndreiO
191  RNA_polymerase_chloroplast      gjo  Folate_Biosynthesis     master:vcrecy
192  Resistance_to_fluoroquinolones  MattC  Formate_dehydrogenase   master:gjo
193  Respiratory_Complex_I   OlgaV  Formate_hydrogenase     master:OlgaV
194  Respiratory_dehydrogenases_1    OlgaV  Fructose-bisphosphate_aldolase_protein_family   master:SvetaG
195  Ribonucleotide_reduction        rodionov  Fucose_and_rhamnose_degradation master:MattC
196  Ribose_and_deoxyribose_phosphate_metabolism     MattC  Fungal_cytostatics      master:OlgaV
197  Ribosome_LSU_bacterial  gjo  Fungal_differentiation_factors  master:OlgaV
198  Ribosome_LSU_eukaryotic_and_archaeal    gjo  Galactitol_degradation  master:MattC
199  Ribosome_SSU_bacterial  gjo  Galactose_degradation   master:MattC
200  Ribosome_SSU_chloroplast        gjo  General_secretory_pathway_(Sec-SRP)_complex_(TC_3.A.5.1.1)      master:MattC
201  Ribosome_SSU_eukaryotic_and_archaeal    gjo  Glutamate,_aspartate_and_asparagine_biosynthesis        master:MattC
202  Ribosome_biogenesis_bacterial   gjo  Glutamate_biosynthesis  master:MattC
203  Serine_Biosynthesis     MikeK  Glutamyl_peptidase?     master:RamyA
204  Siderophore_Aerobactin_and_Ferrichrome_Biosynthesis     MattC  Glutathione_Redox_Metabolism    master:Neema_UCSD
205  Soluble_cytochromes_and_functionally_related_electron_carriers  OlgaV  Glycerol_fermenation_to_1,3-propanediol master:gjo
206  Succinate_dehydrogenase OlgaV  Glycerol_Metabolism     master:MattC
207  Sulfate_assimilation    MattC  Glycerolipid_and_glycerphospholipid_metabolism  master:VasiliyP_UCSD
208  Sulfur_Metabolism       RobE  Glycine_cleavage_system master:MattC
209  TCA_Cycle       OlgaV  Glycine_reductase,_sarcosine_reductase_and_betaine_reductase    master:gjo
210  Terminal_cytochrome_C_oxidases  OlgaV  Glycine_synthesis       master:MikeK
211  Terminal_cytochrome_oxidases    OlgaV  glyoxylate_degradation  master:MattC
212  Thiamin_biosynthesis    rodionov  Glyoxylate_Synthesis    master:RickS
213  Threonine_synthesis     MikeK  Gram-Positive_Extracellular_Nucleases   master:RamyA
214  Tocopherol_Biosynthesis OlgaZ  gram_plus_late_competence       master:alexS
215  Transcription_factors_bacterial gjo  GroEL_GroES     master:MikeK
216  Translation_elongation_factors_eukaryotic_and_archaeal  gjo  Heavy_metal_ion_sensors_and_exporters   master:JenZ
217  Translation_factors_bacterial   gjo  Heme-bound_Iron_Scavenge_Pathway        master:RickS
218  Translation_initiation_factors_eukaryotic_and_archaeal  gjo  Hexitol_degradation     master:MattC
219  Transport_of_Nickel_and_Cobalt  rodionov  Histidine_Biosynthesis  master:RossO
220  Trehalose_biosynthesis  MattC  Histidine_Degradation   master:RossO
221  Tricarballylate_Utilization     RossO  HMG_CoA_Synthesis       master:VeronikaV
222  Tryptophan_synthesis    VeronikaV  Homogentisate_pathway_of_aromatic_compound_degradation  master:OlgaV
223  Tyrosine_synthesis      MikeK  hpa_catabolic_pathway   master:YakovK
224  UDP-N-acetylmuramate_from_Fructose-6-phosphate_Biosynthesis     VasiliyP  Hydrogenases    master:OlgaV
225  Ubiquinone_Biosynthesis OlgaZ  Inorganic_Sulfur_Assimilation   master:ChristianR
226  Ubiquinone_Menaquinone-cytochrome_c_reductase_complexes OlgaV  Inositol_catabolism     master:VeronikaV
227  Urea_decomposition      rodionov  Intercellular_adhesion_SA       master:MattC
228  V-Type_ATP_synthase     RickS  Isoleucine_degradation  master:OlgaZ
229  carnitine_metabolism    MattC  Isoprenoid_Biosynthesis master:OlgaZ
230  cysteine_biosynthesis   RobE  KDO2-Lipid_A_biosynthesis       master:OlgaZ
231  dTDP-rhamnose_synthesis MikeK  Ketogluconate_metabolism        master:MattC
232  fatty_acid_metabolism   MattC  L-ascorbate_degradation master:MattC
233  fatty_acid_oxidation_pathway    MattC  Lactose_degradation     master:MattC
234  glyoxylate_degradation  MattC  Leucine_Biosynthesis_v2 master:AdamF
235  mannose_and_GDP-mannose_metabolism      MattC  Leucine_Degradation_and_HMG-CoA_Metabolism      master:VeronikaV
236  polyisoprenoid_biosynthesis     MattC  Lignine_biosynthesis    master:OlgaV
237  ppGpp_biosynthesis      MikeK  linker_unit-arabinogalactan_synthesis   master:NJ
238  tRNA_aminoacylation     gjo  Lipid_A_biosynthesis    master:OlgaZ
239  tRNA_processing gjo  Lipid_A_modifications   master:OlgaZ
240  tRNA_splicing   gjo  Lipoic_acid_metabolism  master:gjo
241    Lipoteichoic_acid_biosynthesis  master:RamyA
242    Listeria_Pathogenicity_Island_LIPI-1_extended   master:SvetaG
243    Listeria_surface_proteins:_Internalin-like_proteins     master:SvetaG
244    Listeria_surface_proteins:_LPXTG_motif  master:SvetaG
245    LMPTP_YfkJ_cluster      master:AndreiO
246    LMPTP_YwlE_cluster      master:AndreiO
247    LOS_core_oligosaccharide_biosynthesis   master:OlgaZ
248    Lysine_Biosynthesis_DAP_Pathway master:AndreiO
249    Malonate_decarboxylase  master:VeronikaV
250    Mannose-sensitive_hemagglutinin_type_4_pilus    master:RobE
251    Mannose_and_fructose_metabolism master:HanYuC_UCSD
252    mannose_and_GDP-mannose_metabolism      master:MattC
253    Membrane-bound_Ni,_Fe-hydrogenase       master:rodionov
254    Menaquinone_and_Phylloquinone_Biosynthesis      master:OlgaZ
255    Menaquinone_Biosynthesis        master:RickS
256    Mercury_resistance_operon       master:JenZ
257    Methane_metabolism      master:MikeR
258    Methanogenesis  master:gjo
259    Methanogenesis_from_methylated_compounds        master:gjo
260    Methanophenazine_hydrogenase    master:gjo
261    methanopterin_biosynthesis      master:AdamF
262    Methionine_Biosynthesis master:rodionov
263    Methionine_Salvage      master:gjo
264    Methylcitrate_cycle     master:MattC
265    Methylglyoxal_Metabolism        master:OlgaZ
266    MLST    master:RobE
267    Molybdopterin_biosynthesis      master:JenZ
268    mycolic_acid_synthesis  master:NJ
269    N-Acetyl-D-Glucosamine_Utilization      master:OlgaZ
270    N-heterocyclic_aromatic_compound_degradation    master:OlgaV
271    N-linked_Glycosylation_in_Bacteria      master:OlgaZ
272    n-Phenylalkanoic_acid_degradation       master:OlgaV
273    Na(+)-translocating_NADH-quinone_oxidoreductase_and_rnf-like_group_of_electron_transport_complexes      master:OlgaV
274    NAD_and_NADP_cofactor_biosynthesis_global       master:AndreiO
275    NAD_and_NADP_cofactor_biosynthesis_in_pathogens master:AndreiO
276    NAD_and_NADP_paper      master:SvetaG
277    NAD_and_NADP_tutorial_10        master:AndreiO
278    Naphtalene_and_antracene_degradation    master:OlgaV
279    NiFe_hydrogenase_maturation     master:gjo
280    Nitrate_and_nitrite_ammonification      master:rodionov
281    Nitrosative_stress      master:rodionov
282    NusA-TFII_Cluster       master:gjo
283    O-linked_flagella_Glycosylation master:OlgaZ
284    Octadecanoids   master:OlgaV
285    Osmotically_activated_L-carnitine_ABC_transporter_in_Listeria   master:JenZ
286    Oxidative_stress        master:OlgaV
287    Oxidative_stress_(animal_systems)       master:OlgaV
288    Oxidative_stress_in_bacteria    master:OlgaV
289    p-Hydroxybenzoate_degradation   master:OlgaV
290    P-type_ATPase_transporter_potassium_(TC_3.A.3.7.1)      master:MattC
291    P_uptake_(cyanobacteria)        master:acm_at_mit
292    Pentose_phosphate_pathway       master:SvetaG
293    Peptidoglycan_Biosynthesis      master:RickS
294    Phenylacetate_pathway_of_aromatic_compound_degradation  master:OlgaV
295    Phenylalanine_synthesis master:MikeK
296    Phenylpropanoid_compound_degradation    master:OlgaV
297    Phenylpropanoids_general_biosynthesis   master:OlgaV
298    Phenylpropionate_Degradation    master:OlgaV
299    Phosphoglycerate_mutase_protein_family  master:SvetaG
300    Phosphotransferase_enzyme_II_-_Glucose_class_permease   master:JenZ
301    Phosphotransferase_enzyme_II_-_Lactose_class_permease   master:JenZ
302    Phosphotransferase_enzyme_II_-_Mannitol_class_permease  master:JenZ
303    Phosphotransferase_enzyme_II_-_Mannose_family_permease  master:JenZ
304    Photosystem_I   master:SvetaG
305    Photosystem_II  master:SvetaG
306    Phycobilisome   master:OlgaZ
307    Phytoalexin_biosynthesis        master:OlgaV
308    Phytochromes    master:OlgaZ
309    Phytosterol_biosynthesis        master:OlgaV
310    Plastoquinone_Biosynthesis      master:OlgaZ
311    Polyadenylation_bacterial       master:gjo
312    Polyamine_Metabolism    master:InesT_UCSD
313    polyisoprenoid_biosynthesis     master:MattC
314    polyprenyl_synthesis    master:NJ
315    Porphyrin,_Heme,_and_Siroheme_Biosynthesis      master:SvetaG
316    ppGpp_biosynthesis      master:MikeK
317    Proline_Catabolism      master:laszloC
318    Proline_degradation     master:unknown
319    Proline_degradation1    master:unknown
320    Proline_Synthesis       master:RickS
321    Propanediol_utilization master:gjo
322    Prophage-encoded_Exotoxins      master:RamyA
323    Prophage_lysogenic_conversion_modules   master:RamyA
324    Proteasome_archaeal     master:gjo
325    Proteasome_eukaryotic   master:gjo
326    Protection_from_Reactive_Oxygen_Species master:MikeK
327    Protein_Acetylation_and_Deacetylation_in_Bacteria       master:AndreiO
328    Protein_degradation     master:gjo
329    Proteolysis_in_bacteria,_ATP-dependent  master:OlgaZ
330    Protocatechuate_branch_of_beta-ketoadipate_pathway      master:OlgaV
331    Protozoan_cytostatics_and_differentiation_factors       master:OlgaV
332    Pterin_biosynthesis     master:vcrecy
333    Purine_conversions      master:OlgaV
334    pyrimidine_conversions  master:RossO
335    Pyrroloquinoline_Quinone_biosynthesis   master:OlgaZ
336    Pyruvate:ferredoxin_oxidoreductase      master:SvetaG
337    Pyruvate_Alanine_Serine_Interconversions        master:JasonS_UCSD
338    Pyruvate_metabolism_I:_anaplerotic_reactions,_PEP       master:SvetaG
339    Queuosine-Archaeosine_Biosynthesis      master:vcrecy
340    Quinate_degradation     master:OlgaV
341    Quinolinic_acid_and_its_derivatives     master:OlgaV
342    Quorum_Sensing:_Autoinducer-2_Synthesis master:AndrewJ
343    Redox-dependent_regulation_of_nucleus_processes master:OlgaV
344    Resistance_to_fluoroquinolones  master:MattC
345    Resistance_to_Vancomycin        master:MattC
346    Respiratory_Complex_I   master:OlgaV
347    Respiratory_dehydrogenases_1    master:OlgaV
348    Riboflavin_metabolism   master:rodionov
349    Ribonuclease_P_archaeal_and_eukaryal    master:gjo
350    Ribonucleotide_reduction        master:rodionov
351    Ribose_and_deoxyribose_phosphate_metabolism     master:MattC
352    Ribosome_biogenesis_bacterial   master:gjo
353    Ribosome_LSU_bacterial  master:gjo
354    Ribosome_LSU_chloroplast        master:gjo
355    Ribosome_LSU_eukaryotic_and_archaeal    master:gjo
356    Ribosome_LSU_mitochondrial      master:gjo
357    Ribosome_SSU_bacterial  master:gjo
358    Ribosome_SSU_chloroplast        master:gjo
359    Ribosome_SSU_eukaryotic_and_archaeal    master:gjo
360    Ribosome_SSU_mitochondrial      master:gjo
361    RNA_polymerase_archaeal master:gjo
362    RNA_polymerase_archaeal_initiation_factors      master:gjo
363    RNA_polymerase_bacterial        master:gjo
364    RNA_polymerase_chloroplast      master:gjo
365    RNA_polymerase_I        master:gjo
366    RNA_polymerase_II       master:gjo
367    RNA_polymerase_II_initiation_factors    master:gjo
368    RNA_polymerase_III      master:gjo
369    Rrf2_family_transcriptional_regulators  master:rodionov
370    Salicylate_ester_degradation    master:OlgaV
371    Salicylic_acid_biosynthesis1    master:OlgaV
372    Selenocysteine_metabolism       master:gjo
373    Serine_Biosynthesis     master:MikeK
374    Siderophore_Aerobactin_and_Ferrichrome_Biosynthesis     master:MikeK
375    Siderophore_enterobactin_biosynthesis   master:MattC
376    Siderophore_enterobactin_biosynthesis_and_ferric_enterbactin_transport  master:MattC
377    Siderophore_Yersiniabactin_Biosynthesis master:MikeK
378    SLO-NADGH_Locus master:RamyA
379    Sodium_Hydrogen_Antiporter      master:JenZ
380    Soluble_cytochromes_and_functionally_related_electron_carriers  master:OlgaV
381    SpeB-SpeF_extended_regulon      master:RamyA
382    Sphingolipid_biosynthesis       master:JorgeF
383    Spliceosome     master:gjo
384    Spore_Coat      master:RickS
385    Steroid_sulfates        master:OlgaV
386    Streptococcal_Hyaluronic_Acid_Capsule   master:RamyA
387    Streptococcal_Mga_Regulon       master:RamyA
388    Streptococcus_pyogenes_Transcription_Regulators master:RamyA
389    Streptococcus_pyogenes_Virulome master:RamyA
390    Streptolysin_S_Biosynthesis_and_Transport       master:RamyA
391    Streptomycin_biosynthesis       master:OlgaV
392    Suberine_biosynthesis   master:OlgaV
393    Succinate_dehydrogenase master:OlgaV
394    Sucrose_Metabolism      master:MattC
395    Sulfate_assimilation    master:MattC
396    Sulfate_to_Sulfide      master:RobE
397    Sulfur_Metabolism       master:RobE
398    Tannin_biosynthesis     master:OlgaV
399    Taurine_Utilization     master:RobE
400    TCA_Cycle       master:OlgaV
401    Teichoic_acid_Biosynthesis      master:OlgaZ
402    Terminal_cytochrome_C_oxidases  master:OlgaV
403    Terminal_cytochrome_oxidases    master:OlgaV
404    Terpen_biosynthesis     master:OlgaV
405    The_Tartronate_Semialdehyde_Hub master:RossO
406    Thiamin_biosynthesis    master:rodionov
407    Thioredoxin-disulfide_reductase master:gjo
408    Threonine_degradation   master:OlgaV
409    Threonine_synthesis     master:MikeK
410    Tocopherol_Biosynthesis master:OlgaZ
411    Toluene_degradation     master:OlgaV
412    Transcription_factors_bacterial master:gjo
413    Transcription_factors_cyanobacterial_RpoD-like_sigma_factors    master:gjo
414    Translation_elongation_factors_eukaryotic_and_archaeal  master:gjo
415    Translation_factors_bacterial   master:gjo
416    Translation_initiation_factors_eukaryotic_and_archaeal  master:gjo
417    Transport_of_Nickel_and_Cobalt  master:rodionov
418    Trehalose_biosynthesis  master:MattC
419    Triacylglycerol_biosynthesis    master:unknown
420    Triacylglycerol_degradation     master:unknown
421    Tricarballylate_Utilization     master:RossO
422    tRNA_aminoacylation     master:gjo
423    tRNA_aminoacylation,_mitochondrial      master:gjo
424    tRNA_processing master:gjo
425    tRNA_splicing   master:gjo
426    Tryptophan_synthesis    master:VeronikaV
427    Tyrosine_synthesis      master:MikeK
428    Ubiquinone_Biosynthesis master:OlgaZ
429    Ubiquinone_Menaquinone-cytochrome_c_reductase_complexes master:OlgaV
430    UDP-N-acetylmuramate_from_Fructose-6-phosphate_Biosynthesis     master:vasiliyP
431    Universal_GTPases       master:gjo
432    Urea_decomposition      master:rodionov
433    Utilization_of_glutathione_as_a_sulphur_source  master:OlgaV
434    V-Type_ATP_synthase     master:RickS
435    Valine_Biosynthesis     master:Straw
436    Valine_degradation      master:OlgaZ
437    Vibrio_Experimental_Type_III_secretion_system   master:JanelleT
438  //  //
439  END  END
440  ;  ;
441      return split(/\n/,$x);      return split(/\n/,$x);
442  }  }
443    
444    
445  sub choose_best_assignment {  sub choose_best_assignment {
446      my($fig,$parms,$pegs,$external_ids) = @_;      my($fig,$parms,$pegs,$external_ids) = @_;
447      my($peg,$id);      my($peg,$id);
# Line 239  Line 467 
467      if (! $func)                                           { return "hypothetical protein" }      if (! $func)                                           { return "hypothetical protein" }
468      if ($func =~ /^hypothetical (\S+ )?protein .*$/i)      { return "hypothetical protein" }      if ($func =~ /^hypothetical (\S+ )?protein .*$/i)      { return "hypothetical protein" }
469      if ($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)?$/i)     { return "hypothetical protein" }
470        if ($func =~ /^similar to ORF\d+$/)                    { return "hypothetical protein" }
471        if ($func =~ /^(Alr|As|All|Tlr|Tll|Glr|Blr|Slr|SEW|pANL)\d+( protein)?$/i) { return "hypothetical protein" }
472        if ($func =~ /^\d{5}/)                                 { return "hypothetical protein" }
473        if ($func =~ /unknown protein/)                        { return "hypothetical protein" }
474    
475      return $func;      return $func;
476  }  }
# Line 307  Line 539 
539              my $incr = @$x;              my $incr = @$x;
540              foreach $_ (@$x)              foreach $_ (@$x)
541              {              {
542                  if (((100 * $_->[0]) + $incr) > $best_score)                  my($sc,$peg,$in_sub) = @$_;
543                    $sc += $in_sub ? 10000 : 0;
544    
545                    if (((100 * $sc) + $incr) > $best_score)
546                  {                  {
547                      $best_score = (100 * $_->[0]) + $incr;                      $best_score = (100 * $sc) + $incr;
548                      $best_func  = $func;                      $best_func  = $func;
549                      $best_source = $_->[1];                      $best_source = $peg;
550                  }                  }
551              }              }
552          }          }
# Line 348  Line 583 
583          my $subv = 0;          my $subv = 0;
584          my @subs = $fig->peg_to_subsystems($peg);          my @subs = $fig->peg_to_subsystems($peg);
585          my $sub;          my $sub;
586            my $in_sub = 0;
587          foreach $sub (@subs)          foreach $sub (@subs)
588          {          {
589              if (($_ = $parms->{'subsystems'}->{$sub}) && ($_ > $subv))              if ($_ = $parms->{'subsystems'}->{$sub})
590                {
591                    if ($_ > $subv)
592              {              {
593                  $subv = $_;                  $subv = $_;
594              }              }
595                    $in_sub = 1;
596                }
597          }          }
598          $value += $subv;          $value += $subv;
599            push(@{$functions->{$func}},[$value,$peg,$in_sub]);
         push(@{$functions->{$func}},[$value,$peg]);  
600      }      }
601  }  }
602    

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