Table 1. Comparative Analysis of Bce ATCC 14579 and Ban A2012 Based on the Metabolic

Table 1. Comparative analysis of Bce ATCC 14579 and Ban A2012 based on the metabolic reconstruction.

@ Carbohydrate_metabolism

@ Carbohydrate_assimilation

@ Polysaccharide_degradation

@ Pullulan_degradation

* Pullulan_degradation_by_pullulanase

. 3.2.1.41 - Pullulanase

BC2734, BA_3251 95% identical

BC4699, BA_5371 92% identical

@ Chitin_and_chitosan_degradation

* Chitosan_degradation

. Chitosanase (EC 3.2.1.132)

BC2682, BA_3190 96% identical

* Chitin_degradation

. Endochitinase (EC 3.2.1.14)

BC0429, BA_0961 94% identical

. Exochitinase (EC 3.2.1.14)

BC3725, BA_4327 94% identical

@ Degradation_of_inulin_and_levan

* Inulin_oligomer_degradation_by_beta-fructosidase

. 3.2.1.26 - Beta-fructofuranosidase

BC0774, BA_1337 89% identical

@ Glycogen_and_starch_degradation

* Amylose_hydrolysis_via_cyclomaltodextrin

. 3.2.1.54 - Cyclomaltodextrinase

BC4014, BA_4691 93% identical * Amylose_hydrolysis_by_maltogenic_alpha-amylase

. 3.2.1.133 - Glucan 1,4-alpha-maltohydrolase

BC4014, BA_4691 93% identical

* Amylose_hydrolysis_by_maltohexaosidase

. 3.2.1.98 - Glucan 1,4-alpha-maltohexaosidase

BC3482, BA_4041 95% identical

* Amylose_hydrolysis_by_alpha-glucosidase

. 3.2.1.20 - Alpha-glucosidase

BC0413, BA_0945 95% identical

* Amylose_hydrolysis_by_alpha-amylase

. 3.2.1.1 - Alpha-amylase

BC1157, BA_1706 88% identical

* Amylose_phosphorolysis

. 2.4.1.1 - Phosphorylase

BC4863, BA_5537 95% identical

* Glycogen_and_amylopectin_hydrolysis_to_limit_dextrin_by_alpha-amylase

. 3.2.1.1 - Alpha-amylase

BC1157, BA_1706 88% identical

* Glycogen_and_amylopectin_phosphorolysis_to_limit_dextrin

. 2.4.1.1 - Phosphorylase

BC4863, BA_5537 95% identical

@ Assimilation_of_oligosaccharides_and_disaccharides

@ Sucrose_degradation

* Sucrose_hydrolysis

. 3.2.1.26 - Beta-fructofuranosidase

BC0774, BA_1337 89% identical

or . 3.2.1.48 - Sucrose Alpha-glucosidase * Sucrose-6-phosphate_hydrolysis

. 3.2.1.26 - Beta-fructofuranosidase

BC0774, BA_1337 89% identical

@ Degradation_of_alpha-D-glucosyl-D-fructoses

* Palatinose_hydrolysis

. 3.2.1.10 - Oligosaccharide Alpha-1,6-glucosidase

BC4015, BA_4692 95% identical

@ Raffinose_degradation

* Raffinose_degradation_via_beta-fructofuranosidase

. 3.2.1.26 - Beta-fructofuranosidase

BC0774, BA_1337 89% identical

@ Cellobiose_degradation

* Cellobiose_6-phosphate_hydrolysis_via_6-phospho-beta-glucosidase

. 3.2.1.86 - 6-phospho-beta-glucosidase

BC5209, BA_0294 99% identical

BC3760

@ Panose_and_isopanose_degradation

* Panose_hydrolysis_to_glucose_and_maltose

. 3.2.1.70 - Glucan 1,6-alpha-glucosidase

or . 3.2.1.10 - Oligosaccharide Alpha-1,6-glucosidase

BC4015, BA_4692 95% identical

@ Isomaltose_degradation

* Isomaltose_hydrolysis

. 3.2.1.10 - Oligosaccharide Alpha-1,6-glucosidase

BC4015, BA_4692 95% identical

@ Maltose_degradation

* Maltose_acetylation . 2.3.1.79 - Maltose O-acetyltransferase

BC4658, BA_3901 66% identical

* Maltose_hydrolysis

. 3.2.1.20 - Alpha-glucosidase

BC0413, BA_0945 95% identical

or . 3.2.1.48 - Sucrose Alpha-glucosidase

@ Trehalose_degradation

* Trehalose_6-phosphate_hydrolysis

. 3.2.1.93 - Alpha,alpha-phosphotrehalase

BC0632, BA_1215 95% identical

or . 3.2.1.122 - Maltose-6'-phosphate Glucosidase

@ Diacetylchitobiose_and_chitobiose_degradation

* Diacetylchitobiose_uptake_PTS_system

. PTS system, diacetylchitobiose-specific IIA component (EC 2.7.1.69)

BC0807, BA_1377 92% identical

. PTS system, diacetylchitobiose-specific IIB component (EC 2.7.1.69)

BC2393, BA_2957 95% identical

BC0808, BA_1378 94% identical

* Chitobiose-6-phosphate_hydrolysis

. 3.2.1.86 - 6-phospho-beta-glucosidase

BC5209, BA_0294 99% identical

BC3760

@ Glucose_and_gluconate_metabolism

@ Glucose_phosphorylation

* Glucose_phosphorylation_by_glucokinase

. 2.7.1.2 - Glucokinase

BC4260, BA_4934 98% identical * Alpha-phosphoglucomutase_reaction

. 5.4.2.2 - Phosphoglucomutase

BC4919, BA_0026 97% identical

* Glucose-6-phosphate_oxidation_to_6-phosphogluconate

. 1.1.1.49 - Glucose-6-phosphate 1-dehydrogenase

BC3375, BA_3931 97% identical

BC3376, BA_3932 92% identical

. 3.1.1.31 - 6-phosphogluconolactonase, putative

BC3368, BA_3925 91% identical

* D-gluconate_phosphorylation

. 2.7.1.12 - Gluconokinase

BC3369, BA_3926 97% identical

BC2223

BA_0743, BA_0744

* D-glucose_oxidation_by_glucose_1-dehydrogenase

. 1.1.1.47 - Glucose 1-dehydrogenase

BC4715, BA_5386 97% identical

. 3.1.1.17 - Gluconolactonase

@ D-fructose_metabolism

* Fructose_phosphorylation_by_fructokinase

. 2.7.1.4 - Fructokinase

BC0773, BA_1336 88% identical

* D-fructose-1-phosphate_phosphorylation

. 2.7.1.56 - 1-phosphofructokinase

BC3719, BA_4320 90% identical

@ Metabolism_of_D-ribose,_2-deoxy-D-ribose_and_ribitol

* Deoxyribose-phosphate_aldolase . 4.1.2.4 - Deoxyribose-phosphate Aldolase

BC1820, BA_2394 78% identical

* Phosphopentomutase_reaction_(deoxyribose)

. 5.4.2.7 - Phosphopentomutase

BC4087, BA_4767 98% identical

* 2-deoxy-D-ribose_phosphorylation_via_ribokinase

. 2.7.1.15 - Ribokinase

BC0660, BA_1253 95% identical

* Ribokinase

. 2.7.1.15 - Ribokinase

BC0660, BA_1253 95% identical

@ Aminosugar_degradation

@ N-acetylglucosamine_metabolism

* N-acetylglucosamine_phosphorylation_by N-acetylglucosamine_kinase

. 2.7.1.59 - N-acetylglucosamine Kinase

BC2397, BA_2961 79% identical

* N-acetylglucosamine_6-phosphate_deacetylation

. 3.5.1.25 - N-acetylglucosamine-6-phosphate Deacetylase

BC4055, BA_4734 97% identical

* D-glucosamine_6-phosphate_degradation

. 3.5.99.6 - Glucosamine-6-phosphate Deaminase

BC4054, BA_4733 98% identical

@ Uronic_acid_metabolism

* 2-dehydro-3-deoxy-D-gluconate_degradation

. 2.7.1.45 - 2-dehydro-3-deoxygluconokinase

BC4843, BA_5516 95% identical

. 4.1.2.14 - 2-dehydro-3-deoxyphosphogluconate Aldolase BC4844, BA_5517 98% identical

@ Polyol_metabolism

@ Glycerol_and_dihydroxyacetone_metabolism

* Dihydroxyacetone_kinase

. 2.7.1.29 - Glycerone Kinase

BC0981, BA_1540 97% identical

BC0979, BA_1538 94% identical

* Glycerol-3-phosphate_oxidation_to_glycerone-3-phosphate_(NAD(P))

. 1.1.1.94 - Glycerol-3-phosphate Dehydrogenase (nad(p)+)

BC1505, BA_2046 96% identical

. 1.1.1.8 - Glycerol-3-phosphate Dehydrogenase (nad+)

* Glycerol-3-phosphate_oxidation_to_glycerone-3-phosphate_(FAD)

. 1.1.99.5 - Glycerol-3-phosphate Dehydrogenase

BC1036, BA_1587 97% identical

* Glycerol_catabolism_via_EC_2.7.1.30

. 2.7.1.30 - Glycerol Kinase

BC1035, BA_1586 98% identical

@ Myo-inositol_metabolism

* D-inositol_1-phosphate_catabolism

. 3.1.3.25 - Myo-inositol-1(or 4)-monophosphatase

BC3958, BA_4639 94% identical

* Myo-inositol_degradation

. 1.1.1.18 - Myo-inositol 2-dehydrogenase

BA_3002

. IolD protein

BA_3005

. IolB protein BA_3009

. IolE protein

BA_3007

BA_3005

. IolH protein

. IolI protein

. 2.7.1.92 - 5-dehydro-2-deoxygluconokinase

BA_3003

. 4.1.2.29 - 5-dehydro-2-deoxyphosphogluconate Aldolase

BA_3008

. 1.2.1.18 - Malonate-semialdehyde Dehydrogenase (acetylating)

BA_3004

@ Metabolism_of_alcohols,_aldehydes_and_ketones

@ Ethanol_and_acetaldehyde_metabolism

* Ethanol_oxidation_by_alcohol_dehydrogenase

. 1.1.1.1 - Alcohol Dehydrogenase

BC2660, BA_3165 89% identical

BC2220, BA_2770 97% identical

BC0802, BA_1368 92% identical

BC4365, BA_5039 96% identical

* Acetaldehyde_oxidation

. 1.2.1.3 - Aldehyde Dehydrogenase (nad+)

BC3555, BA_4101 98% identical

BC2832, BA_3352 95% identical

or . 1.2.1.4 - Aldehyde Dehydrogenase (nadp+)

* Acetaldehyde_oxidation_(CoA-acetylating)

. 1.2.1.10 - Acetaldehyde Dehydrogenase (acetylating) BC4365, BA_5039 96% identical

@ Methanol_and_formaldehyde_metabolism

* Methanol_oxidation_via_alcohol_dehydrogenase

. 1.1.1.1 - Alcohol Dehydrogenase

BC2660, BA_3165 89% identical

BC2220, BA_2770 97% identical

BC0802, BA_1368 92% identical

BC4365, BA_5039 96% identical

* Formate_biosynthesis

. 1.2.1.1 - Formaldehyde Dehydrogenase (glutathione)

BC3092, BA_3633 98% identical

. 3.1.2.12 - S-formylglutathione Hydrolase

@ Metabolism_of_butane-2,3-diol_and_acetoin

* Acetoin_dehydrogenase_accessory_proteins

. Acetoin utilization protein acuA (EC 2.3.1.-)

BC4660, BA_5335 98% identical

. Acetoin utilization acuB protein

BC4661, BA_5336 98% identical

. Acetoin utilization acuC protein

BC4662, BA_5337 97% identical

* (R,R)-butanediol_oxidation_to_acetoin

. 1.1.1.4 - (r,r)-butanediol Dehydrogenase

BC0668, BA_1262 98% identical

* Acetoin_degradation_to_acetyl-CoA

. 1.2.4.- - Acetoin dehydrogenase E1 component alpha-subunit

BC2779, BA_3300 98% identical

. 1.2.4.- - Acetoin dehydrogenase E1 component beta-subunit BC2778, BA_3299 98% identical

. 2.3.1.- - Dihydrolipoamide acetyltransferase component of acetoin dehydrogenase complex

BC2777, BA_3298 89% identical

. 1.8.1.4 - Dihydrolipoamide Dehydrogenase

BC2776, BA_3297 89% identical

@ Metabolism_of_carboxylic_acids

@ Butyrate_metabolism

* Butanoyl-CoA_biosynthesis_via_butanoyl_phosphate

. 2.7.2.14 - Branched-chain-fatty-acid Kinase

BC4161, BA_4841 97% identical

or . 2.7.2.7 - Butyrate Kinase

. 2.3.1.19 - Phosphate Butyryltransferase

BC4163, BA_4843 96% identical

* Butanoyl-CoA oxidation_via_butyryl-CoA_dehydrogenase

. 1.3.99.2 - Butyryl-CoA Dehydrogenase

BC3074, BA_3608 95% identical

BC5342, BA_0443 97% identical

BC5341, BA_0442 97% identical

* Crotonoyl-CoA--acetyl-CoA_metabolism

. 4.2.1.55 - 3-hydroxybutyryl-coa Dehydratase

BC0898, BA_1476 98% identical

. 1.1.1.157 - 3-hydroxybutyryl-coa Dehydrogenase

BC5343, BA_0444 98% identical

. 2.3.1.9 - Acetyl-coa Acetyltransferase

BC5344, BA_0445 99% identical

@ Propionate_metabolism * Propanoyl-CoA_biosynthesis_via_acetate-CoA_ligase

. 6.2.1.1 - Acetate--coa Ligase

BC4659, BA_5334 98% identical

BC4645, BA_5317 97% identical

BC2489, BA_3055 97% identical

* Methylcitrate_pathway

. 4.1.3.31 - 2-methylcitrate Synthase

BC2285, BA_2844 99% identical

. 4.2.1.79 - 2-methylcitrate Dehydratase

BC2286, BA_2845 99% identical

. 4.2.1.99 - 2-methylisocitrate Dehydratase

BC2286, BA_2845 99% identical

. 4.1.3.30 - Methylisocitrate Lyase

BC2287, RBAT10010 94% identical

* (S)-methylmalonyl-CoA_biosynthesis_via_propionyl-CoA_carboxylase

. 6.4.1.3 - Propionyl-coa Carboxylase

BC2484, BA_3050 97% identical

BC2488, BA_3054 98% identical

* Methylmalonyl-CoA_epimerase

. 5.1.99.1 - Methylmalonyl-coa Epimerase

BC1837, BA_2415 97% identical

@ D-lactate_and_L-lactate_metabolism

* L-lactate_dehydrogenase

. 1.1.1.27 - L-lactate Deydrogenase

BC4996, BA_0106 99% identical

BC1924, BA_2427 99% identical

BC1519 * D-lactate_oxidation_by_(S)-hydroxy-acid_oxidase

. 1.1.3.15 - (s)-2-hydroxy-acid Oxidase

BC1296, BA_1834 96% identical

BC1297, BA_1835 97% identical

BC1303, BA_1841 98% identical

BC3504, BA_4067 93% identical

@ Glycolate_oxidation

* Glyoxylate_reductase

. 1.1.1.79 - Glyoxylate Reductase (nadp+)

BC1415, BA_1955 95% identical

. 1.1.1.26 - Glycolate Reductase

BC1415, BA_1955 95% identical

* Glyoxylate_oxidation_by_(S)-hydroxy-acid_oxidase

. 1.1.3.15 - (s)-2-hydroxy-acid Oxidase

BC1296, BA_1834 96% identical

BC1297, BA_1835 97% identical

BC1303, BA_1841 98% identical

BC3504, BA_4067 93% identical

@ Acetate_assimilation

* Acetyl-CoA_biosynthesis_via_acetate--CoA_ligase

. 6.2.1.1 - Acetate--coa Ligase

BC4659, BA_5334 98% identical

BC4645, BA_5317 97% identical

BC2489, BA_3055 97% identical

* Acetyl-CoA_catabolism_via_acetyl_phosphate

. 2.7.2.1 - Acetate Kinase

BC4637, BA_5309 98% identical . 2.3.1.8 - Phosphate Acetyltransferase

BC5387, BA_0493 99% identical

* 3-phosphoglycerate_anabolism

. 2.7.1.31 - Glycerate Kinase

BC0184, BA_0734 84% identical

* Oxalate_decarboxylation

. 4.1.1.2 - Oxalate Decarboxylase

BC2383, BA_2948 87% identical

BC1031

BA_2254

@ Carbohydrate_membrane_transport

* PTS_system_general_components

. 2.7.3.9 - Phosphoenolpyruvate--protein Phosphatase

BC4048, BA_4726 98% identical

. Phosphocarrier protein HPr

BC4049, BA_4727 100% identical

@ Oligosaccharides_membrane_transport

* Beta-cyclodextrin_uptake_via_cyclodextrin_ABC_transporter

* Alpha-cyclodextrin_uptake_via_cyclodextrin_ABC_transporter

* Linear_maltodextrin_uptake_via_cyclodextrin_ABC_transporter

* Gamma-cyclodextrin_uptake_via_cyclodextrin_ABC_transporter

. Cyclodextrin-binding protein

BC4013, BA_4690 95% identical

. Cyclodextrin transport system permease protein

BC4012, BA_4689 98% identical

BC4011, BA_4688 100% identical

* Lichenan_oligosaccharide_uptake_lic_PTS_system . PTS system, lichenan oligosaccharide-specific IIA component (EC 2.7.1.69)

BC5215, BA_0300 98% identical

BC5210, BA_0295 98% identical

. PTS system, lichenan oligosaccharide-specific IIB component (EC 2.7.1.69)

BC5217, BA_0302 97% identical

. PTS system, lichenan oligosaccharide-specific IIC component

BC5211, BA_0296 99% identical

@ Monosaccharide_membrane_transport

@ Glucose_membrane_transport

* Glucose_uptake_glcBC_PTS_forming_glucose-6-phosphate

. PTS system, glucose-specific IIA component (EC 2.7.1.69)

BC5320, BA_0418 99% identical

. PTS system, glucose-specific IIBC component (EC 2.7.1.69)

* D-glucose_uptake_glucose_transporter_glcU

. Glucose uptake protein

BC4716, BA_5387 97% identical

BC0219, BA_0780 99% identical

@ D-fructose_membrane_transport

* D-fructose_uptake_FruABC_PTS_system

. PTS system, fructose-specific IIABC component (EC 2.7.1.69)

BC3718, BA_4319 94% identical

@ N-acetylglucosamine_membrane_transport

* N-acetylglucosamine_uptake_nag_PTS_forming_GlcNAc-6-phosphate

. PTS system, N-acetylglucosamine-specific IIABC component (EC 2.7.1.69)

BC0482, BA_1071 88% identical

@ Ribose_membrane_transport

* D-ribose_uptake_ribose_ABC_transporter . D-ribose-binding protein

BC0664, BA_1257 97% identical

. Ribose transport system permease protein rbsC

BC2961, BA_3482 95% identical

BC0663, BA_1256 98% identical

. Ribose transport ATP-binding protein rbsA

BC2963, BA_3484 94% identical

. High affinity ribose transport protein rbsD

BC0661, BA_1254 96% identical

@ Carbohydrate_efflux

* Formate_channel

. Formate Transporter

BC3727, BA_4331 93% identical

BC3568, BA_4115 94% identical

@ Aldonic_Uronic_acids_membrane_transport

* D-gluconate_uptake_proton_symport_gluconate_permease

. Gluconate permease

BC4841, BA_5514 98% identical

BC3370, BA_3927 98% identical

@ Disaccharides_membrane_transport

* Diacetylchitobiose_uptake_PTS_system

. PTS system, diacetylchitobiose-specific IIA component (EC 2.7.1.69)

BC0807, BA_1377 92% identical

. PTS system, diacetylchitobiose-specific IIB component (EC 2.7.1.69)

BC2393, BA_2957 95% identical

BC0808, BA_1378 94% identical

. PTS system, diacetylchitobiose-specific IIC component @ Trehalose_membrane_transport

* Trehalose_uptake_glv_PTS_forming_trehalose-6-phosphate

. PTS system, glucose-specific IIA component (EC 2.7.1.69)

BC5320, BA_0418 99% identical

. PTS system, maltose-specific IIBC component (EC 2.7.1.69)

* Trehalose_uptake,_PTS_system

. PTS system, glucose-specific IIA component (EC 2.7.1.69)

BC5320, BA_0418 99% identical

. PTS system, trehalose-specific IIBC component (EC 2.7.1.69)

BC0631, BA_1214 98% identical

@ Sucrose_membrane_transport

* Sucrose_uptake,_PTS_system

. PTS system, glucose-specific IIA component (EC 2.7.1.69)

BC5320, BA_0418 99% identical

. PTS system, sucrose-specific IIBC component (EC 2.7.1.69)

BC0842, BA_1410 96% identical

@ Cellobiose_membrane_transport

* Cellobiose_uptake_lic_PTS_forming_cellobiose-6-phosphate

. PTS system, lichenan oligosaccharide-specific IIA component (EC 2.7.1.69)

BC5215, BA_0300 98% identical

BC5210, BA_0295 98% identical

. PTS system, lichenan oligosaccharide-specific IIB component (EC 2.7.1.69)

BC5217, BA_0302 97% identical

. PTS system, lichenan oligosaccharide-specific IIC component

BC5211, BA_0296 99% identical

@ Salicin_membrane_transport

* Salicin_uptake_lic_PTS_forming_salicin-6-phosphate . PTS system, lichenan oligosaccharide-specific IIA component (EC 2.7.1.69)

BC5215, BA_0300 98% identical

BC5210, BA_0295 98% identical

. PTS system, lichenan oligosaccharide-specific IIB component (EC 2.7.1.69)

BC5217, BA_0302 97% identical

. PTS system, lichenan oligosaccharide-specific IIC component

BC5211, BA_0296 99% identical

@ Arbutin_membrane_transport

* Arbutin_uptake_lic_PTS_forming_arbutin-6-phosphate

. PTS system, lichenan oligosaccharide-specific IIA component (EC 2.7.1.69)

BC5215, BA_0300 98% identical

BC5210, BA_0295 98% identical

. PTS system, lichenan oligosaccharide-specific IIB component (EC 2.7.1.69)

BC5217, BA_0302 97% identical

. PTS system, lichenan oligosaccharide-specific IIC component

BC5211, BA_0296 99% identical

@ Polyols_membrane_transport

@ Glycerol_3-phosphate_membrane_transport

* Glycerol-3-phosphate_uptake_ABC_transporter

. Glycerol-3-phosphate-binding protein

BC0570, BA_1149 84% identical

. SN-glycerol-3-phosphate transport system permease protein ugpA

BC0568, BA_1145 73% identical

. SN-glycerol-3-phosphate transport system permease protein ugpE

BC0569, BA_1147 98% identical

. SN-glycerol-3-phosphate transport ATP-binding protein ugpC

* Glycerol-3-P_phosphate_antiport_glpT . Glycerol-3-phosphate transporter

BC0656, BA_1247 98% identical

* Glycerol_uptake_channel

. Glycerol uptake facilitator protein

BC1034, BA_1585 86% identical

@ Carboxylic_acids_membrane_transport

* Anaerobic_fumarate_uptake_succinate_antiport

. Anaerobic C4-dicarboxylate transporter

BC0421, BA_0954 99% identical

* Anaerobic_fumarate_uptake_proton_symport

. Anaerobic C4-dicarboxylate transporter

BC0421, BA_0954 99% identical

@ Citrate_membrane_transport

* Citrate_uptake_proton_symport

. Citrate-proton symporter

BC0562, BA_1139 94% identical

BC0935, BA_1501 98% identical

* L-lactate_uptake_proton_symport_L-lactate_permease

* Glycolate_uptake_proton_symport_L-lactate_permease

* D-lactate_uptake_proton_symport_L-lactate_permease

. L-lactate permease

BC0612, BA_1194 91% identical

BC1240, BA_1789 96% identical

@ Bacterial_Protein_Metabolism

@ Bacterial_Protein_Degradation

@ Bacterial_metallopeptidases * Bacterial_metallopeptidases

. 3.4.24.3 - Microbial Collagenase

BC4377, BA_5051 95% identical

BC3529, BA_4075 94% identical

BC0556, BA_1129 93% identical

BC3762, BA_4363 90% identical

BC3161, BA_3802 92% identical

BC3412

BC2466

BC3009

BC3010

. 3.4.24.28 - Bacillolysin

BC2735, BA_3252 95% identical

BC0602, BA_1181 95% identical

BC5036, BA_0144 94% identical

BC3383, BA_3938 94% identical

BC5351

BC2167, BA_2678 93% identical

BC2506, BA_3074 82% identical

. 3.4.24.57 - O-sialoglycoprotein Endopeptidase

BC0289, BA_0832 97% identical

. Immune inhibitor A precursor (ec 3.4.24.-)

BC1284, BA_1822 96% identical

BC0666, BA_1259 96% identical

BC2984

. Membrane metalloprotease

BC5377, BA_0481 91% identical BC1446, BA_1986 84% identical

BC3818, BA_4428 94% identical

. Oligoendopeptidase F (ec 3.4.24.-)

BC5453, BA_0564 91% identical

BC1338, BA_1880 90% identical

BC1193, BA_1742 97% identical

BC2870, BA_3391 85% identical

BC2524, BA_3093 95% identical

BC3484, BA_4043 92% identical

BA_3346

. Zinc metalloprotease (ec 3.4.24.-)

BC0369, BA_0908 95% identical

BC1123, BA_1672 94% identical

BC0268, BA_0826 85% identical

. Zinc Protease (ec 3.4.99.-)

BC3803, BA_4413 98% identical

BC3786, BA_4393 95% identical

BC3787, BA_4394 98% identical

. Cell envelope-bound metalloprotease (camelysin) (ec 3.4.24.-)

BC1281, BA_1819 94% identical

BC4868

@ Bacterial_Serine_proteases

* Bacterial_serine_proteases

. 3.4.21.19 - Glutamyl Endopeptidase

BC0789

. 3.4.21.26 - Prolyl Oligopeptidase

BC2927, BA_4352 78% identical . 3.4.21.53 - Endopeptidase La

BC3926, BA_4603 92% identical

BC4478, BA_5142 98% identical

BC4477, BA_5141 98% identical

. 3.4.21.66 - Thermitase

BC2316, BA_2875 96% identical

BC3240

. 3.4.21.89 - Signal Peptidase I

BC1136, BA_1687 93% identical

BC3060, BA_3591 89% identical

BC3837, BA_4447 68% identical

BC3070, BA_3602 97% identical

BC0456, BA_0989 90% identical

BC1278, BA_1816 94% identical

BC2621

. 3.4.21.92 - Endopeptidase Clp

BC2793, BA_3310 96% identical

BC5152, BA_0238 99% identical

BA_4564

. ATP-dependent protease hslV (ec 3.4.25.-)

BC3828, BA_4438 100% identical

. ATP-dependent hsl protease ATP-binding subunit hslU

BC3827, BA_4437 98% identical

. Minor extracellular protease VPR precursor (ec 3.4.21.-)

BC4351, BA_5024 92% identical

BC4869

. Protease Do (ec 3.4.21.-) BC5458, BA_0568 95% identical

. Serine Protease (ec 3.4.21.-)

BC0759, BA_1330 98% identical

BC3927, BA_4604 96% identical

BC2704, BA_3217 91% identical

. Protease Hhoa (ec 3.4.21.-)

BC3600, BA_4148 97% identical

@ Bacterial_Exopeptidases

@ Bacterial_Omega_peptidases

* Bacterial_omega_peptidases

. 3.4.19.1 - Acylaminoacyl-peptidase

BC0192, BA_0747 85% identical

. 3.4.19.3 - Pyroglutamyl-peptidase I

BC3063, BA_3595 94% identical

@ Bacterial_Carboxy_peptidases

* Bacterial_carboxy_peptidases

. 3.4.13.3 - Xaa-his Dipeptidase

BC2439, BA_2989 94% identical

BC4702, BA_5374 94% identical

. 3.4.13.9 - Xaa-pro Dipeptidase

BC4614, BA_5282 99% identical

BC4198, BA_4875 98% identical

BC5199, BA_0284 96% identical

BC3875, BA_4485 90% identical

. 3.4.13.19 - Membrane Dipeptidase

BC3775, BA_4381 92% identical

. 3.4.17.19 - Thermostable Carboxypeptidase 1 BC1566, BA_2104 97% identical

@ Bacterial_Amino_peptidases

* Bacterial_amino_peptidases

. 3.4.11.1 - Leucyl Aminopeptidase

BC4921, BA_0028 96% identical

. 3.4.11.5 - Prolyl Aminopeptidase

BC2171, BA_2719 93% identical

BC4663

BC2337

BA_3206

. 3.4.11.9 - Xaa-pro Aminopeptidase

BC1828, BA_2405 91% identical

. 3.4.11.18 - Methionyl Aminopeptidase

BC5356, BA_0458 98% identical

BC0153, BA_0715 100% identical

BC1568, BA_2107 89% identical

. 3.4.14.11 - Xaa-pro Dipeptidyl-peptidase

BC2861, BA_3381 87% identical

. Aminopeptidase (EC 3.4.11.-)

BC4678, BA_5352 98% identical

BC0360, BA_0899 96% identical

BC1812

. Aminopeptidase Y (EC 3.4.11.-)

BC5359, BA_0463 93% identical

. Deblocking aminopeptidase (EC 3.4.11.-)

BC0901, BA_1479 97% identical

BC4693, BA_5365 98% identical BC4571, BA_5240 98% identical

. Peptidase T (EC 3.4.11.-)

BC3743, BA_4347 95% identical

BC4143, BA_4824 98% identical

@ Amino_acid_membrane_transport

@ Gln_Asn_uptake

* L-glutamine_uptake_Gln_ABC_transporter

. Glutamine-binding protein

BC0640, BA_1224 98% identical

. Glutamine transport system permease protein glnP

BC0642, BA_1226 96% identical

. Glutamine transport ATP-binding protein glnQ

BC0639, BA_1223 95% identical

@ Ser_Thr_uptake

* Serine_uptake_proton_symport_sdaC

. Serine transporter

BC3398, BA_3947 99% identical

BC3189, BA_3808 92% identical

* L-threonine_uptake_LIVTA_ABC_transporter

. Leucine-, isoleucine-, valine-, threonine-, and alanine-binding protein

BC1927, BA_2434 96% identical

. Branched-chain amino acid transport system permease protein livH

BC1930, BA_2437 97% identical

. Branched-chain amino acid transport system permease protein livM

BC1931, BA_2438 97% identical

. Branched-chain amino acid transport ATP-binding protein livG

BC1928, BA_2435 95% identical . Branched-chain amino acid transport ATP-binding protein livF

BC1929, BA_2436 92% identical

@ Cys_Met_uptake

* Cystine_uptake_cystine_ABC_transporter

. Cystine-binding protein

BC0402, BA_0941 95% identical

. Cystine transport system permease protein

BC0873, BA_1436 99% identical

. Cystine transport ATP-binding protein

BC0874, BA_1437 98% identical

@ Ala_Gly_Pro_uptake

* L-alanine_uptake_proton_symport_acp

. Sodium/proton-dependent alanine carrier protein

BC2831, BA_3351 94% identical

BC0638, BA_1222 98% identical

BC5043, BA_0150 96% identical

* Glycine_uptake_sodium_symport_AHdagA

. Na(+)-linked D-alanine glycine permease

BC2317, BA_2876 98% identical

* D-alanine_uptake_sodium_symport_AHdagA

. Na(+)-linked D-alanine glycine permease

BC2317, BA_2876 98% identical

@ Glu_Asp_uptake

* L-glutamate_uptake_proton_sodium_symport_gltT

. Proton/sodium-glutamate symport protein

BC1389, BA_1930 97% identical

BC1739, BA_2304 98% identical BC4242, BA_4917 85% identical

BC5218, BA_0303 99% identical

BC1432, BA_1972 98% identical

* L-aspartate_uptake_proton_sodium_symport_gltT

. Proton/sodium-glutamate symport protein

BC1389, BA_1930 97% identical

BC1739, BA_2304 98% identical

BC4242, BA_4917 85% identical

BC5218, BA_0303 99% identical

BC1432, BA_1972 98% identical

@ Polyamine_transport

* Putrescine_uptake_spermidine-putrescine_ABC_transporter

* Spermidine_uptake_spermidine-putrescine_ABC_transporter

. Spermidine/putrescine-binding protein

BC1289, BA_1827 95% identical

. Spermidine/putrescine transport system permease protein potB

BC1287, BA_1825 95% identical

. Spermidine/putrescine transport system permease protein potC

BC1288, BA_1826 97% identical

. Spermidine/putrescine transport ATP-binding protein potA

BC1286, BA_1824 98% identical

@ Lys_Arg_Orn_uptake

* Diaminopimelate_uptake_cystine_ABC_transporter

. Cystine-binding protein

BC0402, BA_0941 95% identical

. Cystine transport system permease protein

BC0873, BA_1436 99% identical . Cystine transport ATP-binding protein

BC0874, BA_1437 98% identical

* L-arginine_uptake_L-ornithine_antiport

. Arginine/ornithine antiporter

BC0865, BA_1428 98% identical

BC2234, BA_2786 94% identical

BC0629, BA_1212 96% identical

* L-lysine_uptake_proton_symport_lysine_permease

. Lysine-specific permease

BC3052, BA_3583 98% identical

@ Leu_Ile_Val_uptake

* L-leucine_uptake_proton_symport_Leu-Ile-Val_transporter

. Branched-chain amino acid transport system carrier protein

BC0685, BA_1278 76% identical

BC1836, BA_3643 70% identical

BC1441, BA_1981 96% identical

* L-isoleucine_uptake_proton_symport_Leu-Ile-Val_transporter

. Branched-chain amino acid transport system carrier protein

BC0685, BA_1278 76% identical

BC1836, BA_3643 70% identical

BC1441, BA_1981 96% identical

* L-valine_uptake_proton_symport_Leu-Ile-Val_transporter

. Branched-chain amino acid transport system carrier protein

BC0685, BA_1278 76% identical

BC1836, BA_3643 70% identical

BC1441, BA_1981 96% identical

@ Peptide_uptake * Tripeptide_uptake_proton_symport_PTR2

. Di-/tripeptide transporter

BC0684, BA_1277 98% identical

* Dipeptide_uptake_proton_symport_PTR2

. Di-/tripeptide transporter

BC0684, BA_1277 98% identical

* Oligopeptide_uptake_opp_ABC_transporter

. Oligopeptide-binding protein oppA

BC3585, BA_4131 89% identical

BC0215, BA_0775 98% identical

BC0211, BA_0771 96% identical

BC1794, BA_2372 88% identical

BC0241, BA_0798 78% identical

BC2884, BA_3402 74% identical

BC0216, BA_0776 98% identical

BC2848, BA_3371 96% identical

BC0907, BA_1491 97% identical

BC1185, BA_1728 62% identical

BC0859, BA_1422 95% identical

BC2026, BA_2541 95% identical

. Oligopeptide transport system permease protein oppB

BC0242, BA_0799 88% identical

BC2326, BA_2890 96% identical

BC0908, BA_1492 96% identical

BC2222, BA_2772 91% identical

BC0818, BA_1387 94% identical

BC1180, BA_1729 97% identical . Oligopeptide transport system permease protein oppC

BC2327, BA_2891 91% identical

BC0909, BA_1493 97% identical

BC2221, BA_2771 92% identical

BC0819, BA_1388 95% identical

BC1181, BA_1730 98% identical

. Oligopeptide transport ATP-binding protein oppD

BC1182, BA_1731 99% identical

. Oligopeptide transport ATP-binding protein oppF

BC0210, BA_0770 98% identical

BC1183, BA_1732 99% identical

* Amino_acid_uptake,_unknown_specificity,_proton_symport

. Amino acid permease

BC0837, BA_1404 98% identical

BC3245, BA_3819 100% identical

BC3455, BA_4016 98% identical

BC1807, BA_2387 97% identical

BC5013, BA_0124 97% identical

@ Amino_acid_catabolism

@ Degradation_of_aromatic_amino_acids

@ Tryptophan_degradation

* Tryptophan_dioxygenase

. 1.13.11.11 - Tryptophan 2,3-dioxygenase

BC2757, BA_3277 98% identical

* Arylformamidase

. 3.5.1.9 - Arylformamidase sequence not known

@ Kynurenine_degradation * L-kynurenine_hydrolysis

. 3.7.1.3 - Kynureninase

BC2759, BA_3279 95% identical

@ Degradation_of_glutamate,_glutamine,_lysine,_proline_and_arginine

@ Lysine_degradation

* L-lysine_2,3-aminomutase

. 5.4.3.2 - Lysine 2,3-aminomutase

BC2251, BA_2804 99% identical

* L-beta-lysine_degradation_via_beta-lysine_acetyltransferase_(putative)

. Beta-lysine acetyltransferase (EC 2.3.1.-)

BC2249, BA_2802 93% identical

. 6-acetamido-3-oxohexanoate aminotransferase (EC 2.6.1.-)

BC2245, BA_2798 98% identical

. Putative 3-keto-6-acetamidohexanoate cleavage enzyme (EC 2.3.-.-)

BC2247, BA_2800 96% identical

BC2246, BA_2799 98% identical

. 4-acetamidobutyryl-CoA deacetylase-thioesterase (EC 3.-.-.-)

BC2248, BA_2801 95% identical

@ Arginine_degradation

* Arginine_utilization_regulation

. Arginine utilization regulatory protein rocR

BC0473, BA_1064 92% identical

* Arginase

. 3.5.3.1 - Arginase

BC0185, BA_0735 96% identical

* Arginine_degradation_via_arginine_deiminase

. 3.5.3.6 - Arginine Deiminase BC0406

. 2.1.3.3 - Ornithine Carbamoyltransferase

BC0407

BC4126, BA_4808 96% identical

@ Ornithine_degradation

@ D-ornithine_deamination

* D-ornithine_deamination_via_D-alanine_transaminase

. 2.6.1.21 - D-alanine Aminotransferase

BC2209, BA_2758 91% identical

BC5233, BA_0320 73% identical

* D-ornithine_oxidative_deamination

. 1.4.99.1 - D-amino-acid Dehydrogenase

BC2723, BA_3236 95% identical

or . 1.4.3.3 - D-amino Acid Oxidase

* Ornithine_degradation_via_ornithine_cyclodeaminase

. 4.3.1.12 - Ornithine Cyclodeaminase

BC0906, BA_1484 86% identical

* Ornithine--glutamate_degradation

. 2.6.1.13 - Ornithine--oxo-acid Aminotransferase

BC1149, BA_1699 98% identical

. 1.5.1.12 - 1-pyrroline-5-carboxylate Dehydrogenase

BC5006, BA_0116 99% identical

@ L-proline_and_D-proline_degradation

* 4-hydroxy-D-proline_degradation

. 1.4.99.1 - D-amino-acid Dehydrogenase

BC2723, BA_3236 95% identical

or . D-proline oxidase (EC 1.4.-.-) or . 1.4.3.3 - D-amino Acid Oxidase

. 3.5.4.22 - 1-pyrroline-4-hydroxy-2-carboxylate Deaminase

* 4-hydroxy-L-proline_degradation

. 1.5.1.12 - 1-pyrroline-5-carboxylate Dehydrogenase

BC5006, BA_0116 99% identical

. 1.5.1.2 - Pyrroline-5-carboxylate Reductase

BC4134, BA_4817 93% identical

BC3109, BA_3644 92% identical

BC0218, BA_0778 93% identical

. 2.6.1.23 - 4-hydroxyglutamate Aminotransferase sequence not known

. 2.6.1.1 - Aspartate Aminotransferase

BC2896, BA_3415 94% identical

BC4035, BA_4713 96% identical

BC4906, BA_0012 93% identical

. 4.1.3.16 - 4-hydroxy-2-oxoglutarate Aldolase

BC4844, BA_5517 98% identical

* Proline_racemase

. 5.1.1.4 - Proline Racemase

BC2834, BA_3354 92% identical

BC2835, BA_3355 89% identical

BC0905, BA_1483 94% identical

* D-proline_oxidation

. D-proline oxidase (EC 1.4.-.-)

or . 1.4.99.1 - D-amino-acid Dehydrogenase

BC2723, BA_3236 95% identical

or . 1.4.3.3 - D-amino Acid Oxidase

* Proline--glutamate_degradation . 1.5.99.8 - Proline Dehydrogenase

BC5006, BA_0116 99% identical

. 1.5.1.12 - 1-pyrroline-5-carboxylate Dehydrogenase

BC5006, BA_0116 99% identical

@ Glutamine_deamination

* L-glutamine_degradation_via_glutaminase

. 3.5.1.2 - Glutaminase

BC3115, BA_3658 99% identical

BC0481, BA_1070 98% identical

@ Glutamate_degradation

* L-glutamate-D-glutamate.anabolism

. 5.1.1.3 - Glutamate Racemase

BC0866, BA_1429 93% identical

BC4496, BA_5151 99% identical

@ D-glutamate_degradation

* D-alanine_aminotransferase

. 2.6.1.21 - D-alanine Aminotransferase

BC2209, BA_2758 91% identical

BC5233, BA_0320 73% identical

* Gamma-aminobutyrate_shunt

. 4.1.1.15 - Glutamate Decarboxylase

or . 4.1.1.19 - Arginine Decarboxylase

BC0035, BA_0617 87% identical

BC3962, BA_4643 94% identical

. 2.6.1.19 - 4-aminobutyrate Aminotransferase

BC0355, BA_0895 96% identical

. 1.2.1.16 - Succinate-semialdehyde Dehydrogenase (nad(p)+) BC0357, BA_0897 97% identical

BC2241, BA_2794 93% identical

@ Degradation_of_cysteine,_serine_and_alanine

@ Serine_degradation

* L-serine_transamination

. 2.6.1.51 - Serine--pyruvate Aminotransferase

BC2399, BA_2963 88% identical

or . 2.6.1.45 - Serine--glyoxylate Aminotransferase

* L-serine_deamination

. 4.2.1.13 - L-serine Dehydratase

BC4135, BA_4818 99% identical

BC4136, BA_4819 97% identical

. 4.2.1.16 - Threonine Dehydratase

BC2400, RBAT10057 82% identical

BC1781, BA_2357 96% identical

* L-serine_racemization

. Serine racemase (EC 5.1.1.-)

or . 5.1.1.10 - Amino-acid Racemase

or . 5.1.1.1 - Alanine Racemase

BC0264, BA_0822 96% identical

BC2063, BA_2575 94% identical

* D-serine--pyruvate,_NH(,3)_catabolism_(cytosol)

. 4.2.1.14 - D-serine Dehydratase

BC1725, BA_2290 90% identical

@ Alanine_degradation

@ L-alanine_degradation

* L-alanine_oxidative_deamination . 1.4.1.1 - Alanine Dehydrogenase

BC4623, BA_5294 99% identical

BC0592, BA_1174 100% identical

* L-alanine--D-alanine_anabolism

. 5.1.1.1 - Alanine Racemase

BC0264, BA_0822 96% identical

BC2063, BA_2575 94% identical

@ D-alanine_degradation

* D-alanine_aminotransferase

. 2.6.1.21 - D-alanine Aminotransferase

BC2209, BA_2758 91% identical

BC5233, BA_0320 73% identical

* D-alanine_degradation_D-amino_acid_dehydrogenase

. 1.4.99.1 - D-amino-acid Dehydrogenase

BC2723, BA_3236 95% identical

@ Cysteine_desulfuration

* Cysteine--pyruvate,_sulfide,_NH(,3)_catabolism

. 4.4.1.8 - Cystathionine Beta-lyase

BC4366, BA_5041 98% identical

BC4254, BA_4928 96% identical

@ Degradation_of_branched-chain_amino_acids

@ Leucine_degradation

@ Leucine_deamination

* L-leucine_deamination_via_aminotransferases

. 2.6.1.6 - Leucine Aminotransferase sequence not known

or . 2.6.1.42 - Branched-chain Amino Acid Aminotransferase

BC1776, BA_2352 97% identical BC1396, BA_1936 98% identical

* L-leucine_oxidative_deamination_via_leucine_dehydrogenase

. 1.4.1.9 - Leucine Dehydrogenase

BC4162, BA_4842 99% identical

* 2-oxoisocaproate_degradation_via_branched-chain_alpha-keto_acid_dehydrogenase

. 1.2.4.4 - 2-oxoisovalerate Dehydrogenase beta subunit

BC4158, BA_4838 99% identical

. 1.2.4.4 - 2-oxoisovalerate Dehydrogenase alpha subunit

BC4159, BA_4839 97% identical

. Lipoamide acyltransferase component of branched-chain alpha-keto acid dehydrogenase complex (EC 2.3.1.-)

BC4157, BA_4837 98% identical

. 1.8.1.4 - Dihydrolipoamide Dehydrogenase

BC4160, BA_4840 99% identical

* Isovalerate_fermentation

. 2.3.1.19 - Phosphate Butyryltransferase

BC4163, BA_4843 96% identical

. 2.7.2.14 - Branched-chain-fatty-acid Kinase

BC4161, BA_4841 97% identical

@ Valine_degradation

@ Valine_deamination

* L-valine_deamination_via_branched-chain-amino-acid_transaminase

. 2.6.1.42 - Branched-chain Amino Acid Aminotransferase

BC1776, BA_2352 97% identical

BC1396, BA_1936 98% identical

* L-valine_deamination_via_dehydrogenases

. 1.4.1.8 - Valine Dehydrogenase (nadp+) . 1.4.1.9 - Leucine Dehydrogenase

BC4162, BA_4842 99% identical

* Ketovaline--isobutyryl-CoA

. 1.2.4.4 - 2-oxoisovalerate Dehydrogenase beta subunit

BC4158, BA_4838 99% identical

. 1.2.4.4 - 2-oxoisovalerate Dehydrogenase alpha subunit

BC4159, BA_4839 97% identical

. Lipoamide acyltransferase component of branched-chain alpha-keto acid dehydrogenase complex (EC 2.3.1.-)

BC4157, BA_4837 98% identical

. 1.8.1.4 - Dihydrolipoamide Dehydrogenase

BC4160, BA_4840 99% identical

* Isobutyrate_fermentation

. 2.3.1.19 - Phosphate Butyryltransferase

BC4163, BA_4843 96% identical

. 2.7.2.14 - Branched-chain-fatty-acid Kinase

BC4161, BA_4841 97% identical

@ Isoleucine_degradation

@ Isoleucine_deamination

* L-isoleucine_deamination_via_branched-chain-amino-acid_transaminase

. 2.6.1.42 - Branched-chain Amino Acid Aminotransferase

BC1776, BA_2352 97% identical

BC1396, BA_1936 98% identical

* L-isoleucine_oxidative_deamination_via_leucine_dehydrogenase

. 1.4.1.9 - Leucine Dehydrogenase

BC4162, BA_4842 99% identical

* 3-Methyl-2-oxopentanoate--2-methylbutyryl-CoA . 1.2.4.4 - 2-oxoisovalerate Dehydrogenase beta subunit

BC4158, BA_4838 99% identical

. 1.2.4.4 - 2-oxoisovalerate Dehydrogenase alpha subunit

BC4159, BA_4839 97% identical

. Lipoamide acyltransferase component of branched-chain alpha-keto acid dehydrogenase complex (EC 2.3.1.-)

BC4157, BA_4837 98% identical

. 1.8.1.4 - Dihydrolipoamide Dehydrogenase

BC4160, BA_4840 99% identical

* 2-methylbutyrate_fermentation

. 2.3.1.19 - Phosphate Butyryltransferase

BC4163, BA_4843 96% identical

. 2.7.2.14 - Branched-chain-fatty-acid Kinase

BC4161, BA_4841 97% identical

@ Degradation_of_homocysteine,_homoserine_and_threonine

@ Threonine_degradation

* Threonine--glycine_degradation

. 1.1.1.103 - L-threonine 3-dehydrogenase

BC0622, BA_1204 97% identical

. 2.3.1.29 - Glycine C-acetyltransferase

BC0621, BA_1203 99% identical

* Threonine--2-oxobutanoate_degradation

. 4.2.1.16 - Threonine Dehydratase

BC2400, RBAT10057 82% identical

BC1781, BA_2357 96% identical

* Homocysteine--2-oxobutanoate_catabolism

. 4.4.1.1 - Cystathionine Gamma-lyase BC4366, BA_5041 98% identical

* Homoserine--2-oxobutanoate_catabolism

. 4.4.1.1 - Cystathionine Gamma-lyase

BC4366, BA_5041 98% identical

* 2-oxobutanoate_decarboxylation_by_pyruvate_dehydrogenase_complex

. 1.2.4.1 - Pyruvate Dehydrogenase E1 Component alpha subunit

BC3973, BA_4650 98% identical

. 1.2.4.1 - Pyruvate Dehydrogenase E1 Component beta subunit

BC3972, BA_4649 99% identical

. 2.3.1.12 - Dihydrolipoamide Acetyltransferase Component of pyruvate dehydrogenase complex

BC3971, BA_4648 98% identical

. 1.8.1.4 - Dihydrolipoamide dehydrogenase

BC3970, BA_4647 99% identical

@ Degradation_of_glycine_and_sarcosine

* Sarcosine_degradation_by_glycine_oxidase

. Glycine oxidase (ec 1.5.3.-)

BC0747, BA_1318 93% identical

@ Glycine_degradation

* Glycine_decarboxylase_complex

. 1.4.4.2 - Glycine Dehydrogenase (decarboxylating)

BC4225, BA_4902 99% identical

BC4224, BA_4901 97% identical

. 2.1.2.10 - Aminomethyltransferase

BC4226, BA_4903 100% identical

* Glycine_oxidase

BC0747, BA_1318 93% identical @ Degradation_of_histidine,_aspartate_and_asparagine

@ Histidine_degradation

@ Histidine--glutamate_degradation

* Histidine--glutamate,_formamide_catabolism

. 4.3.1.3 - Histidine Ammonia-lyase

BC3652, BA_4195 97% identical

. 4.2.1.49 - Urocanate Hydratase

BC3651, BA_4194 99% identical

. 3.5.2.7 - Imidazolonepropionase

BC3650, BA_4193 99% identical

. 3.5.3.8 - Formiminoglutamase

BC3649, BA_4192 97% identical

* Formamidase

. 3.5.1.49 - Formamidase sequence not known

@ Asparagine_degradation

* Asparaginase

. 3.5.1.1 - Asparaginase

BC3094, BA_3638 98% identical

BC1496, BA_2038 95% identical

@ Aspartate_degradation

* L-aspartate--D-aspartate_anabolism

. 5.1.1.13 - Aspartate Racemase

BC4750, BA_5425 90% identical

BC2177, BA_2726 87% identical

BC2623, BA_3158 94% identical

@ D-aspartate_degradation

* D-aspartate_deamination_via_D-alanine_aminotransferase . 2.6.1.21 - D-alanine Aminotransferase

BC2209, BA_2758 91% identical

BC5233, BA_0320 73% identical

@ Bacterial_Nucleic_acid_metabolism

@ Bacterial_DNA_Repair

@ Bacterial_Excision_Repair

* Nucleotide_Excision_Repair_NER

. Excinuclease ABC subunit A

BC2513, RBAT10056 81% identical

BC5167, BA_0253 99% identical

. Excinuclease ABC subunit B

BC5168, BA_0254 99% identical

. Excinuclease ABC subunit C

BC4520, BA_5187 97% identical

. DNA helicase II (EC 3.6.1.-)

BC0340, BA_0876 98% identical

. DNA polymerase I (EC 2.7.7.7)

BC4587, BA_5255 98% identical

. 6.5.1.2 - Dna Ligase (nad+)

BC0341, BA_0877 98% identical

. 4.2.99.18 - Dna-(apurinic Or Apyrimidinic Site) Lyase

BC1548, BA_2089 94% identical

. Transcription-repair coupling factor

BC0058, BA_0641 98% identical

. DNA repair protein recN

BC4173, RBAT10024 98% identical . Uvr repair protein

BA_3794

BXB0094

. UvrC-like protein

BC2713, BA_3227 87% identical

BC3107, BA_3641 92% identical

. UV-ENDONUCLEASE (UvsE/Uve1/UvdE Family)

BC0260, BA_0818 92% identical

BC5347, BA_0449 90% identical

* Base_Excision_Repair_BER

. 2.1.1.63 - Methylated-dna--[protein]-cysteine S-methyltransferase

BC3741, BA_4345 89% identical

BC2024, BA_2538 87% identical

. Ada Regulatory Protein

BC3740, BA_4344 89% identical

. 3.2.2.21 - Dna-3-methyladenine Glycosylase Ii

BC3742, BA_4346 86% identical

BC0468, BA_1003 94% identical

. Uracil-DNA glycosylase (EC 3.2.2.-)

BC5398, BA_0505 93% identical

. Single-stranded-DNA-specific exonuclease recJ (EC 3.1.-.-)

BC4403, BA_5077 96% identical

. Mutator mutT protein (7,8-dihydro-8-oxoguanine-triphosphatase) (EC 3.6.1.-)

BC5157, BA_0243 100% identical

BC3037, BA_3568 90% identical

. 4.2.99.18 - Dna-(apurinic Or Apyrimidinic Site) Lyase

BC1548, BA_2089 94% identical . 3.2.2.23 - Dna-formamidopyrimidine Glycosylase

BC4586, BA_5254 98% identical

. A/G-specific adenine DNA glycosylase (EC 3.2.2.-)

BC0504, BA_1092 95% identical

. 3.1.11.2 - Exodeoxyribonuclease Iii

BC0415, BA_0947 90% identical

BC3739, BA_4343 94% identical

. 3.1.21.2 - Deoxyribonuclease Iv (phage T4-induced)

BC4282, BA_4956 98% identical

. 6.5.1.2 - Dna Ligase (nad+)

BC0341, BA_0877 98% identical

@ Mismatch_Repair

* Long-Patch_MMR

. DNA mismatch repair protein mutL

BC3768, BA_4374 96% identical

. DNA mismatch repair protein mutS

BC3769, BA_4375 97% identical

BC3480, BA_4039 96% identical

BC4552, BA_5220 98% identical

. Mutator mutT protein (7,8-dihydro-8-oxoguanine-triphosphatase) (EC 3.6.1.-)

BC5157, BA_0243 100% identical

BC3037, BA_3568 90% identical

BC0540, BA_1114 94% identical

. MutT/nudix family protein

BC4636, BA_5308 81% identical

BC2686, BA_3192 83% identical

. A/G-specific adenine DNA glycosylase (EC 3.2.2.-) BC0504, BA_1092 95% identical

. Single-stranded-DNA-specific exonuclease recJ (EC 3.1.-.-)

BC4403, BA_5077 96% identical

. 3.1.11.6 - Exodeoxyribonuclease Vii

BC4179, BA_4856 98% identical

. DNA polymerase III alpha subunit (EC 2.7.7.7)

BC3816, BA_4426 98% identical

BC4605, BA_5272 96% identical

BC3611, BA_4159 92% identical

. DNA polymerase III, epsilon chain (EC 2.7.7.7)

BC3538, BA_4085 87% identical

. DNA polymerase III, beta chain (EC 2.7.7.7)

BC2693, BA_3202 86% identical

BC0002, BA_0597 96% identical

. DNA polymerase III, delta subunit (EC 2.7.7.7)

BC4321, BA_4995 97% identical

. DNA polymerase III, delta' subunit (EC 2.7.7.7)

BC0037, BA_0619 96% identical

. DNA polymerase III subunit gamma/tau (EC 2.7.7.7)

BC0024, BA_0613 96% identical

. Single-strand DNA binding protein

BC5475, BA_0580 98% identical

BC2154, BA_2661 91% identical

* Short-Patch_MMR

. DNA mismatch repair protein mutS

BC3769, BA_4375 97% identical

BC3480, BA_4039 96% identical BC4552, BA_5220 98% identical

. DNA mismatch repair protein mutL

BC3768, BA_4374 96% identical

. DNA polymerase I (EC 2.7.7.7)

BC4587, BA_5255 98% identical

* Recombinational_Repair_RER

. 3.1.11.5 - Exodeoxyribonuclease V

BC4389, BA_5063 98% identical

. ATP-dependent nuclease subunit A

BC1138, BA_1689 97% identical

. ATP-dependent nuclease subunit B

BC1137, BA_1688 96% identical

. Single-stranded-DNA-specific exonuclease recJ (EC 3.1.-.-)

BC4403, BA_5077 96% identical

. ATP-dependent DNA helicase recQ (EC 3.6.1.-)

BC2815, BA_3339 97% identical

BC1485, BA_2026 94% identical

. ATP-dependent DNA helicase recG (EC 3.6.1.-)

BC3853, BA_4464 98% identical

. Regulatory protein recX

BC0498, BA_1086 95% identical

. Recf Protein

BC0004, BA_0599 98% identical

. DNA repair protein recO

BC4295, BA_4969 98% identical

. Recombination protein recR

BC0026, BA_0615 99% identical . Holliday junction DNA helicase ruvA

BC4415, BA_5089 99% identical

. Holliday junction DNA helicase ruvB

BC4414, BA_5088 97% identical

. DNA repair protein recN

BC4173, RBAT10024 98% identical

. DNA polymerase I (EC 2.7.7.7)

BC4587, BA_5255 98% identical

. DNA repair protein radC

BC4461, BA_5125 87% identical

. DNA repair protein RadA

BC0103, BA_0671 99% identical

. Recombination protein recU

BC1554, BA_2092 96% identical

. Primosomal protein N'

BC3866, BA_4477 96% identical

. Primosomal protein dnaI

BC4579, BA_5247 98% identical

. Replicative DNA helicase (EC 3.6.1.-)

BC0956, BA_1513 96% identical

BC5470, BA_0575 97% identical

. DNA primase (EC 2.7.7.-)

BC4290, BA_4965 88% identical

* SOS_Error-Prone_Repair_SOS

. Regulatory protein recX

BC0498, BA_1086 95% identical

. 3.4.21.88 - Repressor Lexa BC3690, BA_4235 100% identical

. ATP-dependent helicase, DinG family

BC1543, BA_2084 91% identical

BC1565, BA_2103 98% identical

. Excinuclease ABC subunit A

BC2513, RBAT10056 81% identical

BC5167, BA_0253 99% identical

. Excinuclease ABC subunit B

BC5168, BA_0254 99% identical

. DNA polymerase IV (EC 2.7.7.7)

BC4142, BA_4822 95% identical

. Recombination protein recR

BC0026, BA_0615 99% identical

. Holliday junction DNA helicase ruvA

BC4415, BA_5089 99% identical

. Holliday junction DNA helicase ruvB

BC4414, BA_5088 97% identical

. ATP-dependent DNA helicase recG (EC 3.6.1.-)

BC3853, BA_4464 98% identical

. Cell division inhibitor

BC0497, BA_1085 90% identical

. Cell division protein ftsZ

BC3906, BA_4515 81% identical

. DinB protein

BC2315, BA_2874 90% identical

@ Bacterial_Direct_Damage_Reversal

* Bacterial_specialized_photorepair . Spore photoproduct lyase (EC 4.1.99.-)

BC4205, BA_4882 97% identical

* Bacterial_photorepair

. 4.1.99.3 - Deoxyribodipyrimidine Photolyase

BC3137, BA_3689 90% identical

* Bacterial_DNA-joining

. 6.5.1.2 - Dna Ligase (nad+)

BC0341, BA_0877 98% identical

* Bacterial_alkylation-damage_repair

. Ada Regulatory Protein

BC3740, BA_4344 89% identical

. 2.1.1.63 - Methylated-dna--[protein]-cysteine S-methyltransferase

BC3741, BA_4345 89% identical

BC2024, BA_2538 87% identical

@ Bacterial_Restriction_Modification

* Restriction_Modification_Type_Mmr

. 5-methylcytosine-specific restriction enzyme MRR (EC 3.1.21.-)

RBAT10021

* Restriction_Modification_Type_Mcr

. 5-methylcytosine-specific restriction enzyme A (EC 3.1.21.-)

BC2144

BC2145

. 5-methylcytosine-specific Restriction Related Enzyme

BC2236, BA_2788 88% identical

* Restriction_Modification_Type_I

. Type I Restriction-modification System Specificity Subunit

BC4458 BC4460

. Type I Restriction-modification System Methylation Subunit

BC4459

. Type I Restriction-modification System Restriction Subunit (ec 3.1.21.3)

BC4456

BC4457

* Restriction_Modification_TypeII

. Type Ii Restriction-modification System Restriction Subunit (ec 3.1.24.1)

BC0939

BC0940

. Type Ii Restriction-modification System Methylation Subunit

BC0941

Pathways from the Integrated Genomics proprietary pathway collection are organized into the functional hierarchy. Only those parts of the functional hierarchy that are discussed in the paper are presented in the table. For Ban CDSs that were not identified by GenBank, Integrated Genomics CDS numbers are used; sequences of these CDSs along with annotations and partial reconstructions of Bce and Ban can be found at http://www.ergo-light.com. CDSs in the table are pairs of close bi-directional best hits from Bce and Ban that are listed according to their functional assignment, which corresponds to the functional role in the pathway. Percent of identity is that of protein sequences.