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 : h2mb4p_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (61 of 83: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 27
  Gene deletion: b1241 b0351 b4069 b4384 b4152 b2297 b2458 b3617 b2407 b1238 b3124 b1612 b1611 b4122 b4138 b4123 b0621 b4381 b2406 b0114 b0755 b3612 b0529 b2492 b0904 b1511 b1206   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.503958 (mmol/gDw/h)
  Minimum Production Rate : 1.929063 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 994.778264
  EX_o2_e : 271.475818
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.161399
  EX_pi_e : 4.344246
  EX_so4_e : 0.126907
  EX_k_e : 0.098369
  EX_mg2_e : 0.004372
  EX_cl_e : 0.002623
  EX_ca2_e : 0.002623
  EX_cu2_e : 0.000357
  EX_mn2_e : 0.000348
  EX_zn2_e : 0.000172
  EX_ni2_e : 0.000163
  EX_cobalt2_e : 0.000013

Product: (mmol/gDw/h)
  EX_fe3_e : 999.991906
  EX_h2o_e : 544.130569
  EX_co2_e : 24.644125
  Auxiliary production reaction : 1.929063
  EX_ac_e : 0.738461
  EX_succ_e : 0.527491
  EX_ura_e : 0.359348
  DM_mththf_c : 0.000226
  DM_5drib_c : 0.000113
  DM_4crsol_c : 0.000112

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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