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

@ Chitin_and_chitosan_degradation

* Chitosan_degradation

. Chitosanase (EC 3.2.1.132)

* Chitin_degradation

. Endochitinase (EC 3.2.1.14)

. Exochitinase (EC 3.2.1.14)

@ Degradation_of_inulin_and_levan

* Inulin_oligomer_degradation_by_beta-fructosidase

. 3.2.1.26 - Beta-fructofuranosidase

@ 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

* Amylose_hydrolysis_by_maltohexaosidase

. 3.2.1.98 - Glucan 1,4-alpha-maltohexaosidase

* Amylose_hydrolysis_by_alpha-glucosidase

. 3.2.1.20 - Alpha-glucosidase

* Amylose_hydrolysis_by_alpha-amylase

. 3.2.1.1 - Alpha-amylase

* Amylose_phosphorolysis

. 2.4.1.1 - Phosphorylase

* Glycogen_and_amylopectin_hydrolysis_to_limit_dextrin_by_alpha-amylase

. 3.2.1.1 - Alpha-amylase

* Glycogen_and_amylopectin_phosphorolysis_to_limit_dextrin

. 2.4.1.1 - Phosphorylase

@ Assimilation_of_oligosaccharides_and_disaccharides

@ Sucrose_degradation

* Sucrose_hydrolysis

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

@ Degradation_of_alpha-D-glucosyl-D-fructoses

* Palatinose_hydrolysis

. 3.2.1.10 - Oligosaccharide Alpha-1,6-glucosidase

@ Raffinose_degradation

* Raffinose_degradation_via_beta-fructofuranosidase

@ Cellobiose_degradation

* Cellobiose_6-phosphate_hydrolysis_via_6-phospho-beta-glucosidase

. 3.2.1.86 - 6-phospho-beta-glucosidase

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

@ Isomaltose_degradation

* Isomaltose_hydrolysis

. 3.2.1.10 - Oligosaccharide Alpha-1,6-glucosidase

@ Maltose_degradation

* Maltose_acetylation . 2.3.1.79 - Maltose O-acetyltransferase

* Maltose_hydrolysis

. 3.2.1.20 - Alpha-glucosidase

or . 3.2.1.48 - Sucrose Alpha-glucosidase

@ Trehalose_degradation

* Trehalose_6-phosphate_hydrolysis

. 3.2.1.93 - Alpha,alpha-phosphotrehalase

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)

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

* Chitobiose-6-phosphate_hydrolysis

. 3.2.1.86 - 6-phospho-beta-glucosidase

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

* Glucose-6-phosphate_oxidation_to_6-phosphogluconate

. 1.1.1.49 - Glucose-6-phosphate 1-dehydrogenase

. 3.1.1.31 - 6-phosphogluconolactonase, putative

* D-gluconate_phosphorylation

. 2.7.1.12 - Gluconokinase

BC2223

BA_0743, BA_0744

* D-glucose_oxidation_by_glucose_1-dehydrogenase

. 1.1.1.47 - Glucose 1-dehydrogenase

. 3.1.1.17 - Gluconolactonase

@ D-fructose_metabolism

* Fructose_phosphorylation_by_fructokinase

. 2.7.1.4 - Fructokinase

* D-fructose-1-phosphate_phosphorylation

. 2.7.1.56 - 1-phosphofructokinase

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

* Deoxyribose-phosphate_aldolase . 4.1.2.4 - Deoxyribose-phosphate Aldolase

* Phosphopentomutase_reaction_(deoxyribose)

. 5.4.2.7 - Phosphopentomutase

* 2-deoxy-D-ribose_phosphorylation_via_ribokinase

. 2.7.1.15 - Ribokinase

* Ribokinase

. 2.7.1.15 - Ribokinase

@ Aminosugar_degradation

@ N-acetylglucosamine_metabolism

* N-acetylglucosamine_phosphorylation_by N-acetylglucosamine_kinase

. 2.7.1.59 - N-acetylglucosamine Kinase

* N-acetylglucosamine_6-phosphate_deacetylation

. 3.5.1.25 - N-acetylglucosamine-6-phosphate Deacetylase

* D-glucosamine_6-phosphate_degradation

. 3.5.99.6 - Glucosamine-6-phosphate Deaminase

@ Uronic_acid_metabolism

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

. 2.7.1.45 - 2-dehydro-3-deoxygluconokinase

. 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

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

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

. 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

* Glycerol_catabolism_via_EC_2.7.1.30

. 2.7.1.30 - Glycerol Kinase

@ Myo-inositol_metabolism

* D-inositol_1-phosphate_catabolism

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

* 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

* Acetaldehyde_oxidation

. 1.2.1.3 - Aldehyde Dehydrogenase (nad+)

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

* Formate_biosynthesis

. 1.2.1.1 - Formaldehyde Dehydrogenase (glutathione)

. 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.-)

. Acetoin utilization acuB protein

. Acetoin utilization acuC protein

* (R,R)-butanediol_oxidation_to_acetoin

. 1.1.1.4 - (r,r)-butanediol Dehydrogenase

* Acetoin_degradation_to_acetyl-CoA

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

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

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

. 1.8.1.4 - Dihydrolipoamide Dehydrogenase

@ Metabolism_of_carboxylic_acids

@ Butyrate_metabolism

* Butanoyl-CoA_biosynthesis_via_butanoyl_phosphate

. 2.7.2.14 - Branched-chain-fatty-acid Kinase

or . 2.7.2.7 - Butyrate Kinase

. 2.3.1.19 - Phosphate Butyryltransferase

* Butanoyl-CoA oxidation_via_butyryl-CoA_dehydrogenase

. 1.3.99.2 - Butyryl-CoA Dehydrogenase

* Crotonoyl-CoA--acetyl-CoA_metabolism

. 4.2.1.55 - 3-hydroxybutyryl-coa Dehydratase

. 1.1.1.157 - 3-hydroxybutyryl-coa Dehydrogenase

. 2.3.1.9 - Acetyl-coa Acetyltransferase

@ Propionate_metabolism * Propanoyl-CoA_biosynthesis_via_acetate-CoA_ligase

. 6.2.1.1 - Acetate--coa Ligase

* Methylcitrate_pathway

. 4.1.3.31 - 2-methylcitrate Synthase

. 4.2.1.79 - 2-methylcitrate Dehydratase

. 4.2.1.99 - 2-methylisocitrate Dehydratase

. 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

* Methylmalonyl-CoA_epimerase

. 5.1.99.1 - Methylmalonyl-coa Epimerase

@ D-lactate_and_L-lactate_metabolism

* L-lactate_dehydrogenase

. 1.1.1.27 - L-lactate Deydrogenase

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

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

@ Glycolate_oxidation

* Glyoxylate_reductase

. 1.1.1.79 - Glyoxylate Reductase (nadp+)

. 1.1.1.26 - Glycolate Reductase

* Glyoxylate_oxidation_by_(S)-hydroxy-acid_oxidase

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

@ Acetate_assimilation

* Acetyl-CoA_biosynthesis_via_acetate--CoA_ligase

. 6.2.1.1 - Acetate--coa Ligase

* Acetyl-CoA_catabolism_via_acetyl_phosphate

. 2.7.2.1 - Acetate Kinase

BC4637, BA_5309 98% identical . 2.3.1.8 - Phosphate Acetyltransferase

* 3-phosphoglycerate_anabolism

. 2.7.1.31 - Glycerate Kinase

* Oxalate_decarboxylation

. 4.1.1.2 - Oxalate Decarboxylase

BC1031

BA_2254

@ Carbohydrate_membrane_transport

* PTS_system_general_components

. 2.7.3.9 - Phosphoenolpyruvate--protein Phosphatase

. Phosphocarrier protein HPr

@ 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

. Cyclodextrin transport system permease protein

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

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

. PTS system, lichenan oligosaccharide-specific IIC component

@ 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)

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

* D-glucose_uptake_glucose_transporter_glcU

. Glucose uptake protein

@ D-fructose_membrane_transport

* D-fructose_uptake_FruABC_PTS_system

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

@ 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)

@ Ribose_membrane_transport

* D-ribose_uptake_ribose_ABC_transporter . D-ribose-binding protein

. Ribose transport system permease protein rbsC

. Ribose transport ATP-binding protein rbsA

. High affinity ribose transport protein rbsD

@ Carbohydrate_efflux

* Formate_channel

. Formate Transporter

@ Aldonic_Uronic_acids_membrane_transport

* D-gluconate_uptake_proton_symport_gluconate_permease

. Gluconate permease

@ Disaccharides_membrane_transport

* Diacetylchitobiose_uptake_PTS_system

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

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

. PTS system, diacetylchitobiose-specific IIC component @ Trehalose_membrane_transport

* Trehalose_uptake_glv_PTS_forming_trehalose-6-phosphate

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

* Trehalose_uptake,_PTS_system

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

@ Sucrose_membrane_transport

* Sucrose_uptake,_PTS_system

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

@ Cellobiose_membrane_transport

* Cellobiose_uptake_lic_PTS_forming_cellobiose-6-phosphate

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

@ Salicin_membrane_transport

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

@ Arbutin_membrane_transport

* Arbutin_uptake_lic_PTS_forming_arbutin-6-phosphate

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

@ Polyols_membrane_transport

@ Glycerol_3-phosphate_membrane_transport

* Glycerol-3-phosphate_uptake_ABC_transporter

. Glycerol-3-phosphate-binding protein

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

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

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

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

* Glycerol_uptake_channel

. Glycerol uptake facilitator protein

@ Carboxylic_acids_membrane_transport

* Anaerobic_fumarate_uptake_succinate_antiport

. Anaerobic C4-dicarboxylate transporter

* Anaerobic_fumarate_uptake_proton_symport

. Anaerobic C4-dicarboxylate transporter

@ Citrate_membrane_transport

* Citrate_uptake_proton_symport

. Citrate-proton symporter

* 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

@ Bacterial_Protein_Metabolism

@ Bacterial_Protein_Degradation

@ Bacterial_metallopeptidases * Bacterial_metallopeptidases

. 3.4.24.3 - Microbial Collagenase

BC3412

BC2466

BC3009

BC3010

. 3.4.24.28 - Bacillolysin

BC5351

. 3.4.24.57 - O-sialoglycoprotein Endopeptidase

. Immune inhibitor A precursor (ec 3.4.24.-)

BC2984

. Membrane metalloprotease

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

. Oligoendopeptidase F (ec 3.4.24.-)

BA_3346

. Zinc metalloprotease (ec 3.4.24.-)

. Zinc Protease (ec 3.4.99.-)

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

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

. 3.4.21.66 - Thermitase

BC3240

. 3.4.21.89 - Signal Peptidase I

BC2621

. 3.4.21.92 - Endopeptidase Clp

BA_4564

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

. ATP-dependent hsl protease ATP-binding subunit hslU

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

BC4869

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

. Serine Protease (ec 3.4.21.-)

. Protease Hhoa (ec 3.4.21.-)

@ Bacterial_Exopeptidases

@ Bacterial_Omega_peptidases

* Bacterial_omega_peptidases

. 3.4.19.1 - Acylaminoacyl-peptidase

. 3.4.19.3 - Pyroglutamyl-peptidase I

@ Bacterial_Carboxy_peptidases

* Bacterial_carboxy_peptidases

. 3.4.13.3 - Xaa-his Dipeptidase

. 3.4.13.9 - Xaa-pro Dipeptidase

. 3.4.13.19 - Membrane Dipeptidase

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

@ Bacterial_Amino_peptidases

* Bacterial_amino_peptidases

. 3.4.11.1 - Leucyl Aminopeptidase

. 3.4.11.5 - Prolyl Aminopeptidase

BC4663

BC2337

BA_3206

. 3.4.11.9 - Xaa-pro Aminopeptidase

. 3.4.11.18 - Methionyl Aminopeptidase

. 3.4.14.11 - Xaa-pro Dipeptidyl-peptidase

. Aminopeptidase (EC 3.4.11.-)

BC1812

. Aminopeptidase Y (EC 3.4.11.-)

. Deblocking aminopeptidase (EC 3.4.11.-)

. Peptidase T (EC 3.4.11.-)

@ Amino_acid_membrane_transport

@ Gln_Asn_uptake

* L-glutamine_uptake_Gln_ABC_transporter

. Glutamine-binding protein

. Glutamine transport system permease protein glnP

. Glutamine transport ATP-binding protein glnQ

@ Ser_Thr_uptake

* Serine_uptake_proton_symport_sdaC

. Serine transporter

* L-threonine_uptake_LIVTA_ABC_transporter

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

. Branched-chain amino acid transport system permease protein livH

. Branched-chain amino acid transport system permease protein livM

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

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

@ Cys_Met_uptake

* Cystine_uptake_cystine_ABC_transporter

. Cystine-binding protein

. Cystine transport system permease protein

. Cystine transport ATP-binding protein

@ Ala_Gly_Pro_uptake

* L-alanine_uptake_proton_symport_acp

. Sodium/proton-dependent alanine carrier protein

* Glycine_uptake_sodium_symport_AHdagA

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

* D-alanine_uptake_sodium_symport_AHdagA

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

@ Glu_Asp_uptake

* L-glutamate_uptake_proton_sodium_symport_gltT

. Proton/sodium-glutamate symport protein

* L-aspartate_uptake_proton_sodium_symport_gltT

. Proton/sodium-glutamate symport protein

@ Polyamine_transport

* Putrescine_uptake_spermidine-putrescine_ABC_transporter

* Spermidine_uptake_spermidine-putrescine_ABC_transporter

. Spermidine/putrescine-binding protein

. Spermidine/putrescine transport system permease protein potB

. Spermidine/putrescine transport system permease protein potC

. Spermidine/putrescine transport ATP-binding protein potA

@ Lys_Arg_Orn_uptake

* Diaminopimelate_uptake_cystine_ABC_transporter

. Cystine-binding protein

. Cystine transport system permease protein

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

* L-arginine_uptake_L-ornithine_antiport

. Arginine/ornithine antiporter

* L-lysine_uptake_proton_symport_lysine_permease

. Lysine-specific permease

@ Leu_Ile_Val_uptake

* L-leucine_uptake_proton_symport_Leu-Ile-Val_transporter

. Branched-chain amino acid transport system carrier protein

* L-isoleucine_uptake_proton_symport_Leu-Ile-Val_transporter

* L-valine_uptake_proton_symport_Leu-Ile-Val_transporter

@ Peptide_uptake * Tripeptide_uptake_proton_symport_PTR2

. Di-/tripeptide transporter

* Dipeptide_uptake_proton_symport_PTR2

. Di-/tripeptide transporter

* Oligopeptide_uptake_opp_ABC_transporter

. Oligopeptide-binding protein oppA

. Oligopeptide transport system permease protein oppB

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

. Oligopeptide transport ATP-binding protein oppD

. Oligopeptide transport ATP-binding protein oppF

* Amino_acid_uptake,_unknown_specificity,_proton_symport

. Amino acid permease

@ Amino_acid_catabolism

@ Degradation_of_aromatic_amino_acids

@ Tryptophan_degradation

* Tryptophan_dioxygenase

. 1.13.11.11 - Tryptophan 2,3-dioxygenase

* Arylformamidase

. 3.5.1.9 - Arylformamidase sequence not known

@ Kynurenine_degradation * L-kynurenine_hydrolysis

. 3.7.1.3 - Kynureninase

@ Degradation_of_glutamate,_glutamine,_lysine,_proline_and_arginine

@ Lysine_degradation

* L-lysine_2,3-aminomutase

. 5.4.3.2 - Lysine 2,3-aminomutase

* L-beta-lysine_degradation_via_beta-lysine_acetyltransferase_(putative)

. Beta-lysine acetyltransferase (EC 2.3.1.-)

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

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

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

@ Arginine_degradation

* Arginine_utilization_regulation

. Arginine utilization regulatory protein rocR

* Arginase

. 3.5.3.1 - Arginase

* Arginine_degradation_via_arginine_deiminase

. 3.5.3.6 - Arginine Deiminase BC0406

. 2.1.3.3 - Ornithine Carbamoyltransferase

BC0407

@ Ornithine_degradation

@ D-ornithine_deamination

* D-ornithine_deamination_via_D-alanine_transaminase

. 2.6.1.21 - D-alanine Aminotransferase

* D-ornithine_oxidative_deamination

. 1.4.99.1 - D-amino-acid Dehydrogenase

or . 1.4.3.3 - D-amino Acid Oxidase

* Ornithine_degradation_via_ornithine_cyclodeaminase

. 4.3.1.12 - Ornithine Cyclodeaminase

* Ornithine--glutamate_degradation

. 2.6.1.13 - Ornithine--oxo-acid Aminotransferase

. 1.5.1.12 - 1-pyrroline-5-carboxylate Dehydrogenase

@ L-proline_and_D-proline_degradation

* 4-hydroxy-D-proline_degradation

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

. 1.5.1.2 - Pyrroline-5-carboxylate Reductase

. 2.6.1.23 - 4-hydroxyglutamate Aminotransferase sequence not known

. 2.6.1.1 - Aspartate Aminotransferase

. 4.1.3.16 - 4-hydroxy-2-oxoglutarate Aldolase

* Proline_racemase

. 5.1.1.4 - Proline Racemase

* D-proline_oxidation

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

or . 1.4.99.1 - D-amino-acid Dehydrogenase

or . 1.4.3.3 - D-amino Acid Oxidase

* Proline--glutamate_degradation . 1.5.99.8 - Proline Dehydrogenase

@ Glutamine_deamination

* L-glutamine_degradation_via_glutaminase

. 3.5.1.2 - Glutaminase

@ Glutamate_degradation

* L-glutamate-D-glutamate.anabolism

. 5.1.1.3 - Glutamate Racemase

@ D-glutamate_degradation

* D-alanine_aminotransferase

* Gamma-aminobutyrate_shunt

. 4.1.1.15 - Glutamate Decarboxylase

or . 4.1.1.19 - Arginine Decarboxylase

. 2.6.1.19 - 4-aminobutyrate Aminotransferase

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

@ Degradation_of_cysteine,_serine_and_alanine

@ Serine_degradation

* L-serine_transamination

. 2.6.1.51 - Serine--pyruvate Aminotransferase

or . 2.6.1.45 - Serine--glyoxylate Aminotransferase

* L-serine_deamination

. 4.2.1.13 - L-serine Dehydratase

. 4.2.1.16 - Threonine Dehydratase

* L-serine_racemization

. Serine racemase (EC 5.1.1.-)

or . 5.1.1.10 - Amino-acid Racemase

or . 5.1.1.1 - Alanine Racemase

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

. 4.2.1.14 - D-serine Dehydratase

@ Alanine_degradation

@ L-alanine_degradation

* L-alanine_oxidative_deamination . 1.4.1.1 - Alanine Dehydrogenase

* L-alanine--D-alanine_anabolism

. 5.1.1.1 - Alanine Racemase

@ D-alanine_degradation

* D-alanine_aminotransferase

* D-alanine_degradation_D-amino_acid_dehydrogenase

@ Cysteine_desulfuration

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

. 4.4.1.8 - Cystathionine Beta-lyase

@ 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

* L-leucine_oxidative_deamination_via_leucine_dehydrogenase

. 1.4.1.9 - Leucine Dehydrogenase

* 2-oxoisocaproate_degradation_via_branched-chain_alpha-keto_acid_dehydrogenase

. 1.2.4.4 - 2-oxoisovalerate Dehydrogenase beta subunit

. 1.2.4.4 - 2-oxoisovalerate Dehydrogenase alpha subunit

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

* Isovalerate_fermentation

@ Valine_degradation

@ Valine_deamination

* L-valine_deamination_via_branched-chain-amino-acid_transaminase

. 2.6.1.42 - Branched-chain Amino Acid Aminotransferase

* L-valine_deamination_via_dehydrogenases

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

* Ketovaline--isobutyryl-CoA

. 1.2.4.4 - 2-oxoisovalerate Dehydrogenase beta subunit

* Isobutyrate_fermentation

@ Isoleucine_degradation

@ Isoleucine_deamination

* L-isoleucine_deamination_via_branched-chain-amino-acid_transaminase

. 2.6.1.42 - Branched-chain Amino Acid Aminotransferase

* L-isoleucine_oxidative_deamination_via_leucine_dehydrogenase

. 1.4.1.9 - Leucine Dehydrogenase

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

* 2-methylbutyrate_fermentation

@ Degradation_of_homocysteine,_homoserine_and_threonine

@ Threonine_degradation

* Threonine--glycine_degradation

. 1.1.1.103 - L-threonine 3-dehydrogenase

. 2.3.1.29 - Glycine C-acetyltransferase

* Threonine--2-oxobutanoate_degradation

. 4.2.1.16 - Threonine Dehydratase

* 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

* 2-oxobutanoate_decarboxylation_by_pyruvate_dehydrogenase_complex

. 1.2.4.1 - Pyruvate Dehydrogenase E1 Component alpha subunit

. 1.2.4.1 - Pyruvate Dehydrogenase E1 Component beta subunit

. 2.3.1.12 - Dihydrolipoamide Acetyltransferase Component of pyruvate dehydrogenase complex

. 1.8.1.4 - Dihydrolipoamide dehydrogenase

@ Degradation_of_glycine_and_sarcosine

* Sarcosine_degradation_by_glycine_oxidase

. Glycine oxidase (ec 1.5.3.-)

@ Glycine_degradation

* Glycine_decarboxylase_complex

. 1.4.4.2 - Glycine Dehydrogenase (decarboxylating)

. 2.1.2.10 - Aminomethyltransferase

* 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

. 4.2.1.49 - Urocanate Hydratase

. 3.5.2.7 - Imidazolonepropionase

. 3.5.3.8 - Formiminoglutamase

* Formamidase

. 3.5.1.49 - Formamidase sequence not known

@ Asparagine_degradation

* Asparaginase

. 3.5.1.1 - Asparaginase

@ Aspartate_degradation

* L-aspartate--D-aspartate_anabolism

. 5.1.1.13 - Aspartate Racemase

@ D-aspartate_degradation

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

@ Bacterial_Nucleic_acid_metabolism

@ Bacterial_DNA_Repair

@ Bacterial_Excision_Repair

* Nucleotide_Excision_Repair_NER

. Excinuclease ABC subunit A

. Excinuclease ABC subunit B

. Excinuclease ABC subunit C

. DNA helicase II (EC 3.6.1.-)

. DNA polymerase I (EC 2.7.7.7)

. 6.5.1.2 - Dna Ligase (nad+)

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

. Transcription-repair coupling factor

. DNA repair protein recN

BC4173, RBAT10024 98% identical . Uvr repair protein

BA_3794

BXB0094

. UvrC-like protein

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

* Base_Excision_Repair_BER

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

. Ada Regulatory Protein

. 3.2.2.21 - Dna-3-methyladenine Glycosylase Ii

. Uracil-DNA glycosylase (EC 3.2.2.-)

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

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

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

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

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

. 3.1.11.2 - Exodeoxyribonuclease Iii

. 3.1.21.2 - Deoxyribonuclease Iv (phage T4-induced)

@ Mismatch_Repair

* Long-Patch_MMR

. DNA mismatch repair protein mutL

. DNA mismatch repair protein mutS

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

. MutT/nudix family protein

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

. 3.1.11.6 - Exodeoxyribonuclease Vii

. DNA polymerase III alpha subunit (EC 2.7.7.7)

. DNA polymerase III, epsilon chain (EC 2.7.7.7)

. DNA polymerase III, beta chain (EC 2.7.7.7)

. DNA polymerase III, delta subunit (EC 2.7.7.7)

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

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

. Single-strand DNA binding protein

* Short-Patch_MMR

. DNA mismatch repair protein mutS

. DNA mismatch repair protein mutL

* Recombinational_Repair_RER

. 3.1.11.5 - Exodeoxyribonuclease V

. ATP-dependent nuclease subunit A

. ATP-dependent nuclease subunit B

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

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

. Regulatory protein recX

. Recf Protein

. DNA repair protein recO

. Recombination protein recR

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

. Holliday junction DNA helicase ruvB

. DNA repair protein recN

. DNA repair protein radC

. DNA repair protein RadA

. Recombination protein recU

. Primosomal protein N'

. Primosomal protein dnaI

. Replicative DNA helicase (EC 3.6.1.-)

. DNA primase (EC 2.7.7.-)

* SOS_Error-Prone_Repair_SOS

. Regulatory protein recX

. 3.4.21.88 - Repressor Lexa BC3690, BA_4235 100% identical

. ATP-dependent helicase, DinG family

. Excinuclease ABC subunit A

. Excinuclease ABC subunit B

. DNA polymerase IV (EC 2.7.7.7)

. Recombination protein recR

. Holliday junction DNA helicase ruvA

. Holliday junction DNA helicase ruvB

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

. Cell division inhibitor

. Cell division protein ftsZ

. DinB protein

@ Bacterial_Direct_Damage_Reversal

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

* Bacterial_photorepair

. 4.1.99.3 - Deoxyribodipyrimidine Photolyase

* Bacterial_DNA-joining

* Bacterial_alkylation-damage_repair

. Ada Regulatory Protein

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

@ 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

* 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.