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 : 2ombzl_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (47 of 85: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 25
  Gene deletion: b3399 b1241 b0351 b4069 b2744 b3115 b1849 b2296 b3617 b0160 b1612 b1611 b4122 b4374 b0675 b2361 b2291 b0261 b0114 b0755 b3612 b0529 b2492 b0904 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.413826 (mmol/gDw/h)
  Minimum Production Rate : 0.144231 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 994.144791
  EX_o2_e : 279.599102
  EX_glc__D_e : 10.000000
  EX_nh4_e : 4.469290
  EX_pi_e : 0.399179
  EX_so4_e : 0.104210
  EX_k_e : 0.080776
  EX_mg2_e : 0.003590
  EX_ca2_e : 0.002154
  EX_cl_e : 0.002154
  EX_cu2_e : 0.000293
  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_fe3_e : 999.993354
  EX_h2o_e : 546.095478
  EX_co2_e : 32.143139
  EX_fum_e : 0.720554
  EX_ac_e : 0.605052
  Auxiliary production reaction : 0.144231
  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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