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 : 12ppd__S_e
List of minimal gene deletion strategies (Download)

Gene deletion strategy (70 of 92: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 33
  Gene deletion: b3553 b1478 b4382 b1241 b0351 b4384 b0871 b3115 b1849 b2296 b2407 b3844 b1004 b3713 b1109 b0046 b3236 b1779 b2210 b1033 b3945 b1602 b0153 b0529 b2492 b0904 b3035 b1380 b2660 b1517 b0606 b2285 b1010   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.499228 (mmol/gDw/h)
  Minimum Production Rate : 0.058246 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 995.404880
  EX_o2_e : 288.203501
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.391615
  EX_pi_e : 0.481558
  EX_so4_e : 0.125715
  EX_k_e : 0.097446
  EX_mg2_e : 0.004331
  EX_ca2_e : 0.002598
  EX_cl_e : 0.002598
  EX_cu2_e : 0.000354
  EX_mn2_e : 0.000345
  EX_zn2_e : 0.000170
  EX_ni2_e : 0.000161
  EX_cobalt2_e : 0.000012

Product: (mmol/gDw/h)
  EX_fe3_e : 999.991982
  EX_h2o_e : 552.450077
  EX_co2_e : 39.330122
  EX_12ppd__S_e : 0.059254
  EX_mththf_e : 0.000224
  DM_5drib_c : 0.000112
  DM_4crsol_c : 0.000111

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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