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 : nadph_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (65 of 80: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 38
  Gene deletion: b2836 b3553 b3399 b2744 b3708 b3008 b0871 b0160 b1982 b2797 b3117 b1814 b4471 b1033 b4374 b0675 b2361 b2291 b0261 b0507 b3709 b3161 b0112 b0114 b0886 b2366 b2492 b0904 b2578 b1533 b3927 b2965 b0693 b1473 b0594 b4141 b1798 b0221   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.746439 (mmol/gDw/h)
  Minimum Production Rate : 0.171334 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 24.597242
  EX_glc__D_e : 10.000000
  EX_nh4_e : 9.261657
  EX_pi_e : 1.234023
  EX_so4_e : 0.187968
  EX_k_e : 0.145700
  EX_fe2_e : 0.011989
  EX_mg2_e : 0.006475
  EX_ca2_e : 0.003885
  EX_cl_e : 0.003885
  EX_cu2_e : 0.000529
  EX_mn2_e : 0.000516
  EX_zn2_e : 0.000255
  EX_ni2_e : 0.000241
  EX_cobalt2_e : 0.000019

Product: (mmol/gDw/h)
  EX_h2o_e : 49.071828
  EX_co2_e : 25.760737
  EX_h_e : 7.716925
  Auxiliary production reaction : 0.171334
  DM_oxam_c : 0.000835
  DM_5drib_c : 0.000501
  DM_4crsol_c : 0.000166

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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