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 : 2dr5p_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (59 of 75: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 29
  Gene deletion: b4269 b3942 b1732 b0493 b3588 b3003 b3011 b1241 b0351 b1479 b0871 b3617 b3236 b1779 b3962 b3946 b2210 b0825 b4267 b2799 b4381 b2868 b0114 b0529 b2492 b0904 b0508 b4266 b1518   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.446493 (mmol/gDw/h)
  Minimum Production Rate : 1.452640 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 31.748759
  EX_glc__D_e : 10.000000
  EX_nh4_e : 4.822082
  EX_pi_e : 1.883329
  EX_so4_e : 0.112436
  EX_k_e : 0.087152
  EX_fe2_e : 0.007171
  EX_mg2_e : 0.003873
  EX_cl_e : 0.002324
  EX_ca2_e : 0.002324
  EX_cu2_e : 0.000317
  EX_mn2_e : 0.000309
  EX_zn2_e : 0.000152
  EX_ni2_e : 0.000144
  EX_cobalt2_e : 0.000011

Product: (mmol/gDw/h)
  EX_h2o_e : 46.867463
  EX_co2_e : 33.624189
  EX_h_e : 4.102552
  Auxiliary production reaction : 1.452640
  EX_acald_e : 0.392571
  DM_mththf_c : 0.000200
  DM_5drib_c : 0.000100
  DM_4crsol_c : 0.000100

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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