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 : duri_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (21 of 50: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 26
  Gene deletion: b1478 b1241 b0351 b3831 b4069 b0910 b2930 b4232 b3697 b3925 b0871 b2297 b2458 b2926 b3617 b1238 b2690 b2143 b2498 b0675 b0822 b4381 b0114 b2492 b0904 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.340119 (mmol/gDw/h)
  Minimum Production Rate : 0.061563 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 990.149618
  EX_o2_e : 281.150926
  EX_glc__D_e : 10.000000
  EX_nh4_e : 4.284532
  EX_pi_e : 0.328081
  EX_so4_e : 0.085649
  EX_k_e : 0.066389
  EX_mg2_e : 0.002951
  EX_ca2_e : 0.001770
  EX_cl_e : 0.001770
  EX_cu2_e : 0.000241
  EX_mn2_e : 0.000235
  EX_zn2_e : 0.000116
  EX_ni2_e : 0.000110

Product: (mmol/gDw/h)
  EX_fe3_e : 999.994537
  EX_h2o_e : 543.593166
  EX_co2_e : 28.900036
  EX_pyr_e : 4.368582
  EX_ac_e : 1.251765
  DM_oxam_c : 0.488149
  Auxiliary production reaction : 0.061563
  DM_5drib_c : 0.000077
  DM_4crsol_c : 0.000076

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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