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 : udpLa4fn_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (73 of 82: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 32
  Gene deletion: b1241 b0351 b3831 b1278 b3614 b0910 b3752 b4152 b2297 b2458 b2781 b1612 b1611 b4122 b1779 b1759 b3616 b3589 b2440 b4138 b4123 b0621 b4381 b2406 b0755 b3612 b2492 b0904 b3918 b0418 b1206 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.445600 (mmol/gDw/h)
  Minimum Production Rate : 0.235341 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 994.572508
  EX_o2_e : 285.870057
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.679773
  EX_pi_e : 0.900511
  EX_so4_e : 0.112211
  EX_k_e : 0.086978
  EX_mg2_e : 0.003866
  EX_cl_e : 0.002319
  EX_ca2_e : 0.002319
  EX_cu2_e : 0.000316
  EX_mn2_e : 0.000308
  EX_zn2_e : 0.000152
  EX_ni2_e : 0.000144
  EX_cobalt2_e : 0.000011

Product: (mmol/gDw/h)
  EX_fe3_e : 999.992843
  EX_h2o_e : 551.218942
  EX_co2_e : 35.998766
  EX_succ_e : 0.464668
  Auxiliary production reaction : 0.235341
  EX_ura_e : 0.080655
  DM_5drib_c : 0.000100
  DM_4crsol_c : 0.000099

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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