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 : hemeO_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (56 of 98: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 37
  Gene deletion: b4467 b2242 b4382 b0474 b2518 b3831 b4384 b1278 b3752 b2925 b2097 b2781 b1004 b3713 b1109 b0046 b1612 b1611 b4122 b1779 b2690 b1759 b2210 b4161 b1415 b0411 b3945 b4138 b4123 b0621 b3028 b1380 b3918 b1206 b2285 b3893 b1474   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.418215 (mmol/gDw/h)
  Minimum Production Rate : 0.036813 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 32.565540
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.036213
  EX_pi_e : 0.403413
  EX_so4_e : 0.105315
  EX_k_e : 0.081633
  EX_fe2_e : 0.043530
  EX_mg2_e : 0.003628
  EX_ca2_e : 0.002177
  EX_cl_e : 0.002177
  EX_cu2_e : 0.000297
  EX_mn2_e : 0.000289
  EX_zn2_e : 0.000143
  EX_ni2_e : 0.000135
  EX_cobalt2_e : 0.000010

Product: (mmol/gDw/h)
  EX_h2o_e : 46.640995
  EX_co2_e : 33.309968
  EX_h_e : 7.997937
  EX_ac_e : 2.615184
  EX_succ_e : 0.436111
  EX_ura_e : 0.186137
  Auxiliary production reaction : 0.036813
  EX_for_e : 0.001026
  DM_5drib_c : 0.000094
  DM_4crsol_c : 0.000093

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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