Table 3.
List of 30 biochemical reactions available in SrapWT2040 (wild-type), but absent in SrapUV2010 (SRMK07 strain).
| Metabolic pathway | Reaction ID | Protein name | Reactiona |
|---|---|---|---|
| Fructose and mannose metabolism | XYLI1 | Xylose isomerase | xyl__D_c ⇔ xylu__D_c |
| Fructose and mannose metabolism | XYLI2 | Xylose isomerase | glc__D_c ⇔ fru_c |
| Glyoxylate and dicarboxylate metabolism | TRSARr | Tartronate semialdehyde reductase | 2h3oppan_c + h_c + nadh_c ⇔ glyc__R_c + nad_c |
| Glyoxylate and dicarboxylate metabolism | HPYRI | Hydroxypyruvate isomerase | hpyr_c ⇔ 2h3oppan_c |
| Carbohydrate acid metabolism | GLCRD | Glucarate dehydratase | glcr_c → 5dh4dglc_c + h2o_c |
| TCA cycle | FRD8 | Fumarate reductase (menaquione-9) | fum_c + mql9_c → mqn9_c + succ_c |
| Phenylalanine metabolism | PHACTE | Phenylacetyl-CoA thioesterase | h2o_c + phaccoa_c → coa_c + h_c + pac_c |
| Sulfur metabolism | TAUDO | Taurine dioxygenase | akg_c + o2_c + taur_c → aacald_c + co2_c + h_c + so3_c + succ_c |
| Benzoate degradation | 3OADPCOAT | 3-Oxoadipate CoA-transferase | 3oxoadp_c + succoa_c → oxadpcoa_c + succ_c |
| Arginine and proline metabolism | AGMDA | Agmatine deiminase | agm_c + h2o_c → cptrc_c + nh4_c |
| Arginine and proline metabolism | AGMT | Agmatinase | agm_c + h2o_c → ptrc_c + urea_c |
| Calcium-dependent antibiotic biosynthesis | CDAS12 | Hexenoyl-CoA monooxygenase | h_c + hx2coa_c + nadph_c + o2_c → ephxcoa_c + h2o_c + nadp_c |
| Lipoate salvage I | LIPAMPL | Lipoyl-adenylate protein ligase | lipoamp_c → amp_c + h_c + lipopb_c |
| Lipoate salvage I | LIPATPT | Lipoate-ATP adenylate transferase | atp_c + lipoate_c → lipoamp_c + ppi_c |
| Lipoate metabolism | OCTNLL | Octanoate non-lipoylated apo domain ligase | atp_c + h_c + octa_c → amp_c + octapb_c + ppi_c |
| Glycine, serine and threonine metabolism | GLYAT | Glycine C-acetyltransferase | accoa_c + gly_c ⇔ 2aobut_c + coa_c |
| Ascorbate and aldarate metabolism | GLCRD2 | d-glucarate hydro-lyase | glcr_c ⇔ 2dh3dglc_c + h2o_c |
| Styrene degradation | R05551 | Acrylamidase | aa_c + h2o_c ⇔ acryl_c + nh4_c |
| Transport reaction | HOMt2 | l-homoserineserine efflux via proton symport | h_e + hom__L_c → h_c + hom__L_e |
| Synthesis and degradation of ketone bodies; Valine, leucine and isoleucine degradation; Butanoate metabolism | OCOAT1 | 3-Oxoacid CoA-transferase (Succinyl-CoA: acetoacetate) | acac_c + succoa_c → aacoa_c + succ_c |
| Dioxin degradation; Polycyclic aromatic hydrocarbon degradation; Naphthalene degradation | SALOR | Salicylate 1-monooxygenase | 2.0 h_c + nadh_c + o2_c + salc_c → catechol_c + co2_c + h2o_c + nad_c |
| Biosynthesis of secondary metabolites | ACTS16 | actVA-5/actVB monooxygenase | ddhkACPact_c + o2_c → dhkACPact_c + h2o_c |
| Biosynthesis of secondary metabolites | ACTS17 | R09312 | dhkACPact_c + h2o_c + nadh_c → ACPact_c + dhkdhqn_c + nad_c |
| Biosynthesis of secondary metabolites | ACTS18 | Dihydrokalafungin-dihydroquinone,FMNH2:oxygen oxidoreductase (hydroxylating) | dhkdhqn_c + fmnh2_c + o2_c ⇔ fmn_c + h2o_c + hdhk_c |
| Biosynthesis of secondary metabolites | ACTS16b | R09314 | ddhkACPact_c + fmnh2_c + o2_c → dhkACPact_c + fmn_c + h2o_c + 2.0 h_c |
| Biosynthesis of secondary metabolites | R00918 | Propanoyl-CoA:(2S)-methylmalonyl-CoA malonyltransferase (cyclizing); | MNXM2496_c + 6.0 co2_c + 7.0 coa_c + h2o_c + 6.0 nadp_c ⇔ 12.0 h_c + 6.0 mmcoa__S_c + 6.0 nadph_c + ppcoa_c |
| Biosynthesis of secondary metabolites | R02225 | ATP:streptomycin 6-phosphotransferase | Stmyn_c + atp_c ⇔ MNXM2286_c + adp_c + h_c |
| Biosynthesis of secondary metabolites | R07253 | Acyl-CoA:malonyl-CoA C-acyltransferase (decarboxylating, oxoacyl-reducing, thioester-hydrolysing and cyclizing) | MNXM2093_c + 3.0 co2_c + 4.0 coa_c + h2o_c + nadp_c ⇔ accoa_c + 3.0 h_c + 3.0 malcoa_c + nadph_c |
| NODOx | Nitric oxide dioxygenase | nadh_c + 2.0 no_c + 2.0 o2_c → h_c + nad_c + 2.0 no3_c | |
| NODOy | Nitric oxide dioxygenase | nadph_c + 2.0 no_c + 2.0 o2_c → h_c + nadp_c + 2.0 no3_c |
aMetabolite abbreviations: 2aobut_cL-2-amino-3-oxobutanoate, 2dh3dglc_c 2-dehydro-3-deoxy-D-glucarate, 2h3oppan_c 2-hydroxy-3-oxopropanoate, 3oxoadp_c 3-oxoadipate, 5dh4dglc_c5-dehydro-4-deoxy-D-glucarate, MNXM2093_c 6-methylsalicylate, MNXM2286_cstreptomycin 6-phosphate, MNXM2496_c 6-deoxyerythronolide B, Stmyn_c streptomycin, aa_c acrylamide, aacald_c aminoacetaldehyde, aacoa_c acetoacetyl-CoA,acac_c acetoacetate, accoa_c acetyl-CoA, ACPact_c acyl carrier protein (specific to actinorhodin PKS), acryl_c acrylate,adp_c ADP, agm_c agmatine, akg_c 2-oxoglutarate, amp_c AMP,atp_c ATP, catechol_c catechol, co2_c CO2, coa_c coenzyme A, cptrc_c N-carbamoylputrescine, ddhkACPact_c 6-deoxydihydrokalafungin, dhkACPact_c dihydrokalafungin, dhkdhqn_c dihydrokalafungin dihydroquinone form, ephxcoa_c trans-2,3-epoxyhexanoyl-CoA, fmn_c flavin mononucelotide, fmnh2_c reduced FMN, fru_c D-fructose, fum_c fumarate, glc__D_c d-glucose, glcr_c d-glucarate, gly_c glycine, glyc__R_c (R)-glycerate, h2o_c H2O, h_c H + , h_e H + , hdhk_c hydroxylated dihydrokalafungin, hom__L_c l-homoserine, hpyr_c hydroxypyruvate, hx2coa_c trans-hex-2-enoyl-CoA, lipoamp_c lipoyl-AMP, lipoate_c lipoate, lipopb_c protein N6-(lipoyl)lysine, malcoa_c malonyl-CoA, mmcoa__S_c (S)-methylmalonyl-CoA, mql9_c menaquinol 9, mqn9_c menaquinone 9, nad_c nicotinamide adenine dinucleotide, nadh_c nicotinamide adenine dinucleotide—reduced, nadp_c nicotinamide adenine dinucleotide phosphate, nadph_c nicotinamide adenine dinucleotide phosphate—reduced, nh4_c ammonium, no_c nitric oxide, no3_c nitrate, o2_c O2, octa_c octanoate (n-C8:0), octapb_c protein N6-(octanoyl)lysine, oxadpcoa_c3-oxoadipyl-CoA,pac_c phenylacetic acid, phaccoa_c phenylacetyl-CoA, ppcoa_c propanoyl-CoA, ppi_c diphosphate, ptrc_c putrescine, salc_c salicylate, so3_c sulfite, succ_c succinate, succoa_c succinyl-CoA, taur_c taurine, urea_c urea, xyl__D_c d-xylose, xylu__D_cD-xylulose.