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 : datp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (90 of 114: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 33
  Gene deletion: b3553 b3399 b2744 b3926 b2930 b4232 b3697 b3925 b0871 b2297 b2458 b1004 b3713 b1109 b0046 b3236 b1779 b2690 b2210 b1033 b3945 b1602 b4381 b0114 b0529 b2492 b0904 b1380 b2660 b1517 b0606 b2285 b4209   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.368319 (mmol/gDw/h)
  Minimum Production Rate : 0.038800 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 30.346336
  EX_glc__D_e : 10.000000
  EX_nh4_e : 4.171817
  EX_pi_e : 0.471683
  EX_so4_e : 0.092750
  EX_k_e : 0.071893
  EX_mg2_e : 0.003195
  EX_fe2_e : 0.003040
  EX_fe3_e : 0.002876
  EX_ca2_e : 0.001917
  EX_cl_e : 0.001917
  EX_cu2_e : 0.000261
  EX_mn2_e : 0.000255
  EX_zn2_e : 0.000126
  EX_ni2_e : 0.000119

Product: (mmol/gDw/h)
  EX_h2o_e : 44.011093
  EX_co2_e : 28.367873
  EX_h_e : 8.878703
  EX_pyr_e : 5.375163
  Auxiliary production reaction : 0.038800
  DM_mththf_c : 0.000165
  DM_5drib_c : 0.000083
  DM_4crsol_c : 0.000082

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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