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 : xan_e
List of minimal gene deletion strategies (Download)

Gene deletion strategy (89 of 94: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 43
  Gene deletion: b3553 b1478 b0238 b0125 b1241 b4069 b0512 b3115 b1849 b2296 b2926 b1004 b3713 b1109 b0046 b3236 b1638 b0477 b4139 b1033 b2799 b3945 b1602 b0507 b4381 b3915 b3654 b3714 b3664 b0511 b4064 b4464 b0529 b2492 b0904 b2954 b3029 b1380 b2660 b1517 b0221 b2285 b1007   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.473300 (mmol/gDw/h)
  Minimum Production Rate : 0.331065 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 38.347005
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.435856
  EX_pi_e : 0.456548
  EX_so4_e : 0.119186
  EX_k_e : 0.092385
  EX_fe3_e : 0.007602
  EX_mg2_e : 0.004106
  EX_cl_e : 0.002464
  EX_ca2_e : 0.002464
  EX_cu2_e : 0.000336
  EX_mn2_e : 0.000327
  EX_zn2_e : 0.000161
  EX_ni2_e : 0.000153
  EX_cobalt2_e : 0.000012

Product: (mmol/gDw/h)
  EX_h2o_e : 53.840061
  EX_co2_e : 38.365741
  EX_h_e : 5.956276
  EX_xan_e : 0.331065
  EX_ac_e : 0.275548
  DM_mththf_c : 0.000212
  DM_5drib_c : 0.000106
  DM_4crsol_c : 0.000106

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.

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Last updated: 21-Sep-2023
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