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 (44 of 103: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 30
  Gene deletion: b3553 b3399 b1241 b0351 b4069 b2502 b2744 b2297 b2458 b1238 b1004 b3713 b1109 b0046 b1982 b3616 b3589 b2210 b1033 b0675 b2361 b0261 b1602 b4381 b0114 b0529 b2492 b0904 b1380 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.405315 (mmol/gDw/h)
  Minimum Production Rate : 1.196730 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 32.054009
  EX_glc__D_e : 10.000000
  EX_nh4_e : 7.484464
  EX_pi_e : 1.587699
  EX_so4_e : 0.102066
  EX_k_e : 0.079115
  EX_fe2_e : 0.006510
  EX_mg2_e : 0.003516
  EX_ca2_e : 0.002110
  EX_cl_e : 0.002110
  EX_cu2_e : 0.000287
  EX_mn2_e : 0.000280
  EX_zn2_e : 0.000138
  EX_ni2_e : 0.000131
  EX_cobalt2_e : 0.000010

Product: (mmol/gDw/h)
  EX_h2o_e : 52.166814
  EX_co2_e : 32.142275
  EX_h_e : 7.067262
  Auxiliary production reaction : 1.196730
  EX_thymd_e : 0.356820
  EX_ac_e : 0.235969
  DM_5drib_c : 0.000272
  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.

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Last updated: 21-Sep-2023
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