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 : pg120_p
List of minimal gene deletion strategies (Download)

Gene deletion strategy (60 of 77: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 29
  Gene deletion: b4382 b3831 b4384 b3614 b0910 b3752 b4152 b2925 b2097 b2781 b3844 b1232 b1612 b1611 b4122 b1759 b3946 b0825 b4138 b4123 b0621 b2406 b0452 b2197 b3825 b3918 b4042 b1206 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.533115 (mmol/gDw/h)
  Minimum Production Rate : 0.105477 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 996.487713
  EX_h_e : 989.818178
  EX_o2_e : 278.884730
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.513716
  EX_pi_e : 0.619723
  EX_so4_e : 0.134249
  EX_k_e : 0.104060
  EX_mg2_e : 0.004625
  EX_ca2_e : 0.002775
  EX_cl_e : 0.002775
  EX_cu2_e : 0.000378
  EX_mn2_e : 0.000368
  EX_zn2_e : 0.000182
  EX_ni2_e : 0.000172
  EX_cobalt2_e : 0.000013

Product: (mmol/gDw/h)
  EX_fe3_e : 996.479150
  EX_h2o_e : 546.192664
  EX_co2_e : 31.217815
  EX_succ_e : 0.555928
  EX_ura_e : 0.378058
  Auxiliary production reaction : 0.105477
  DM_5drib_c : 0.000120
  DM_4crsol_c : 0.000119

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.

Last updated: 21-Sep-2023
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