MetNetComp Database [1] / Core Genes A set of core genes for simulation-based growth-coupled production. You can also see minimal gene deletions.

Model : iML1515 [2].
Target metabolite : ugmd_c
Core genes for growth-coupled production (at least stoichioemetrically feasible)
  #Remaining genes : 309
  Remaining genes: b2551 b0870 b3368 b2436 b1260 b0109 b1094 b2472 b2935 b1261 b3426 b4054 b3770 b3281 b0243 b0414 b3041 b0025 b3812 b1662 b0421 b3804 b0469 b3997 b3187 b0339 b4006 b2508 b2400 b3993 b1062 b1281 b0639 b0720 b1136 b2103 b4226 b3057 b4053 b3642 b0415 b3648 b3771 b4383 b3952 b1854 b3951 b3197 b3972 b0071 b0072 b3671 b3670 b0908 b1263 b1264 b2599 b2600 b2329 b3633 b1262 b0174 b0524 b0963 b0182 b1702 b4025 b0915 s0001 b0767 b3386 b0073 b2464 b2026 b0523 b1131 b2024 b3607 b2414 b4214 b2762 b2582 b2827 b3940 b3433 b3639 b2838 b0475 b4040 b3974 b0103 b1693 b2942 b1215 b3198 b0417 b1098 b0521 b0888 b1210 b0522 b2029 b2687 b3960 b3172 b0242 b0074 b3958 b1091 b0154 b0918 b0159 b3176 b3730 b3189 b3967 b2763 b0386 b2764 b2323 b2507 b0142 b3634 b0778 b0173 b1812 b3360 b3843 b2478 b4039 b0337 b3729 b2415 b2416 b2312 b0171 b1740 b2780 b4254 b2500 b0087 b0090 b3774 b2316 b3255 b0185 b3256 b0052 b2564 b2615 b0369 b4005 b2557 b3957 b4177 b3744 b4245 b1852 b0029 b0134 b0420 b1092 b3809 b0031 b0003 b1208 b2746 b3359 b0004 b4013 b1704 b2750 b2904 b0116 b2905 b1622 b2903 b3939 b1377 b3956 b3608 b0179 b0085 b0091 b1277 b0088 b2752 b2751 b0726 b0727 b0131 b0086 b0096 b0181 b2019 b2020 b2022 b1207 b0010 b2417 b0763 b2153 b0764 b0765 b1101 b1250 b3805 b2747 b1761 b3731 b3736 b3732 b3738 b3733 b3737 b3735 b3734 b4067 b2023 b2025 b3640 b3772 b3479 b3477 b3476 b3480 b3478 b4094 b0048 b0388 b0114 b0115 b0774 b2315 b0612 b2818 b0381 b4019 b0133 b2476 b3389 b3941 b2574 b3177 b3919 b2914 b0750 b3870 b0914 b1967 b1865 b3850 b2133 b3959 b2499 b1380 b0954 b1288 b0175 b0089 b1069 b2585 b1093 b0149 b0635 b0084 b2021 b0166 b3994 b0429 b0432 b0431 b0430 b4041 b0180 b3018 b3572 b4160 b1276 b4297 b0268 b2987 b3040 b3196 b0155 b1378 b2895 b0777 b0641 b3201 b3200 b4261 b4262 b3199 b0054 b2530 b2529 b3058 b2528 b0775 b3991 b3992 b0423 b3990 b4407 b0776 b3412 b2515 b4238   (List of alternative genes)
  Computed by: AddGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.262122 (mmol/gDw/h)
  Minimum Production Rate : 0.138438 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 30.952520
  EX_glc__D_e : 10.000000
  EX_nh4_e : 3.898495
  EX_pi_e : 0.529721
  EX_so4_e : 0.066008
  EX_k_e : 0.051164
  EX_mg2_e : 0.002274
  EX_fe2_e : 0.002163
  EX_fe3_e : 0.002047
  EX_ca2_e : 0.001364
  EX_cl_e : 0.001364
  EX_cu2_e : 0.000186
  EX_mn2_e : 0.000181
  EX_zn2_e : 0.000089
  EX_ni2_e : 0.000085

Product: (mmol/gDw/h)
  EX_h2o_e : 43.668265
  EX_co2_e : 29.400491
  EX_h_e : 8.379037
  EX_pyr_e : 3.649428
  EX_acald_e : 0.671187
  EX_succ_e : 0.549380
  EX_ac_e : 0.152604
  Auxiliary production reaction : 0.138438
  EX_ura_e : 0.047445
  EX_ala__D_e : 0.003642
  DM_mththf_c : 0.000117
  EX_dxylnt_e : 0.000117
  DM_5drib_c : 0.000059
  DM_4crsol_c : 0.000058

Visualization
  1. Download JSON file.
  2. Go to Escher site [3].
  3. Select "Data > Load reaction data" and apply the downloaded file.

References
[1] Tamura, T. MetNetComp: Database for minimal and maximal gene deletion strategies for growth-coupled production of genome-scale metabolic networks, IEEE/ACM Transactions on Computational Biology and Bioinformatics, in press.
[2] Norsigian, C. J., Pusarla, N., McConn, J. L., Yurkovich, J. T., Dräger, A., Palsson, B. O., & King, Z. (2020). BiGG Models 2020: multi-strain genome-scale models and expansion across the phylogenetic tree. Nucleic acids research, 48(D1), D402-D406.
[3] King, Z. A., Dräger, A., Ebrahim, A., Sonnenschein, N., Lewis, N. E., & Palsson, B. O. (2015). Escher: a web application for building, sharing, and embedding data-rich visualizations of biological pathways. PLoS computational biology, 11(8), e1004321.

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Last updated: 21-Sep-2023
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