MetNetComp Database [1] / Minimal gene deletions

Minimal gene deletions for simulation-based growth-coupled production. You can also see maximal gene deletions.

Model : iML1515 [2].
Target metabolite : dpcoa_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (72 of 80: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 48
  Gene deletion: b4467 b2836 b1478 b4382 b1241 b4069 b4384 b3708 b3752 b3115 b1849 b2296 b2779 b2407 b1004 b3713 b1109 b0046 b3236 b2797 b3117 b1814 b4471 b3665 b0411 b2799 b3945 b1602 b2342 b3845 b2913 b2406 b3915 b3654 b3714 b3664 b1539 b2492 b0904 b1533 b1380 b1511 b4141 b1798 b0606 b2285 b1010 b4209   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.414238 (mmol/gDw/h)
  Minimum Production Rate : 0.230765 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 36.096220
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.087323
  EX_pi_e : 0.860603
  EX_so4_e : 0.334827
  EX_k_e : 0.080856
  EX_fe3_e : 0.006655
  EX_mg2_e : 0.003594
  EX_ca2_e : 0.002156
  EX_cl_e : 0.002156
  EX_cu2_e : 0.000294
  EX_mn2_e : 0.000286
  EX_zn2_e : 0.000141
  EX_ni2_e : 0.000134
  EX_cobalt2_e : 0.000010

Product: (mmol/gDw/h)
  EX_h2o_e : 52.297170
  EX_co2_e : 37.212390
  EX_h_e : 4.976052
  EX_ac_e : 0.471677
  Auxiliary production reaction : 0.230513
  DM_mththf_c : 0.000186
  DM_5drib_c : 0.000093
  DM_4crsol_c : 0.000092

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.

Last updated: 21-Sep-2023
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