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 : ditp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (47 of 82: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 25
  Gene deletion: b2836 b3399 b4069 b2502 b2744 b3708 b2297 b2458 b2926 b1982 b2797 b3117 b1814 b4471 b0675 b2361 b4381 b2868 b0114 b1539 b2492 b0904 b1533 b3927 b1511   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.676130 (mmol/gDw/h)
  Minimum Production Rate : 0.201798 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 28.365403
  EX_glc__D_e : 10.000000
  EX_nh4_e : 8.182380
  EX_pi_e : 1.257592
  EX_so4_e : 0.170263
  EX_k_e : 0.131976
  EX_fe2_e : 0.010859
  EX_mg2_e : 0.005865
  EX_ca2_e : 0.003519
  EX_cl_e : 0.003519
  EX_cu2_e : 0.000479
  EX_mn2_e : 0.000467
  EX_zn2_e : 0.000231
  EX_ni2_e : 0.000218
  EX_cobalt2_e : 0.000017

Product: (mmol/gDw/h)
  EX_h2o_e : 49.992343
  EX_co2_e : 29.350471
  EX_h_e : 7.082824
  EX_ac_e : 0.393634
  Auxiliary production reaction : 0.201798
  EX_xan_e : 0.017692
  EX_ade_e : 0.000455
  DM_mththf_c : 0.000303
  DM_5drib_c : 0.000152
  DM_4crsol_c : 0.000151

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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