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 : trp__L_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (17 of 116: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 36
  Gene deletion: b4382 b4069 b4384 b3708 b3008 b3752 b2297 b2458 b2407 b1982 b2688 b2797 b3117 b1814 b4471 b0261 b3709 b2406 b3161 b0112 b0452 b0114 b1539 b2492 b0904 b0591 b2578 b1533 b3927 b1473 b0515 b4141 b1798 b3662 b0221 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.537319 (mmol/gDw/h)
  Minimum Production Rate : 0.341411 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 32.245073
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.488231
  EX_pi_e : 0.518302
  EX_so4_e : 0.135308
  EX_k_e : 0.104881
  EX_fe2_e : 0.008630
  EX_mg2_e : 0.004661
  EX_ca2_e : 0.002797
  EX_cl_e : 0.002797
  EX_cu2_e : 0.000381
  EX_mn2_e : 0.000371
  EX_zn2_e : 0.000183
  EX_ni2_e : 0.000174
  EX_cobalt2_e : 0.000013

Product: (mmol/gDw/h)
  EX_h2o_e : 50.485360
  EX_co2_e : 33.560745
  EX_h_e : 5.935152
  Auxiliary production reaction : 0.341411
  EX_ac_e : 0.312820
  EX_alltn_e : 0.000601
  DM_5drib_c : 0.000361
  DM_4crsol_c : 0.000120

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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