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 : imacp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (102 of 103: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 48
  Gene deletion: b4467 b3399 b4382 b3942 b1732 b4069 b2502 b4384 b2744 b3708 b2297 b2458 b2925 b2097 b3844 b1004 b3713 b1109 b0046 b2797 b3117 b1814 b4471 b3946 b2210 b0825 b3665 b0675 b2361 b2291 b1602 b2406 b0452 b3654 b3714 b3664 b1727 b0114 b2366 b0529 b2492 b0904 b1533 b3927 b1380 b1518 b0606 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.403660 (mmol/gDw/h)
  Minimum Production Rate : 0.514309 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 990.799166
  EX_o2_e : 280.825483
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.388110
  EX_pi_e : 0.903681
  EX_so4_e : 0.101650
  EX_k_e : 0.078792
  EX_mg2_e : 0.003502
  EX_ca2_e : 0.002101
  EX_cl_e : 0.002101
  EX_cu2_e : 0.000286
  EX_mn2_e : 0.000279
  EX_zn2_e : 0.000138
  EX_ni2_e : 0.000130
  EX_cobalt2_e : 0.000010

Product: (mmol/gDw/h)
  EX_fe3_e : 999.993517
  EX_h2o_e : 545.173520
  EX_co2_e : 31.431368
  EX_ac_e : 4.456746
  Auxiliary production reaction : 0.514309
  EX_mththf_e : 0.000181
  DM_5drib_c : 0.000091
  DM_4crsol_c : 0.000090

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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