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 (80 of 82: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 37
  Gene deletion: b2242 b3553 b4382 b0474 b2518 b4384 b2744 b2779 b2781 b1004 b3713 b1109 b0046 b1612 b1611 b4122 b0907 b1759 b2210 b1033 b4374 b4161 b0675 b1415 b4138 b4123 b0621 b2406 b0452 b3825 b3028 b3918 b4042 b1206 b2285 b3893 b1474   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.446229 (mmol/gDw/h)
  Minimum Production Rate : 0.235637 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 994.564612
  EX_o2_e : 285.835480
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.687754
  EX_pi_e : 0.901710
  EX_so4_e : 0.112369
  EX_k_e : 0.087101
  EX_mg2_e : 0.003871
  EX_cl_e : 0.002323
  EX_ca2_e : 0.002323
  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 : 999.992833
  EX_h2o_e : 551.205733
  EX_co2_e : 35.964290
  EX_succ_e : 0.465324
  Auxiliary production reaction : 0.235637
  EX_ura_e : 0.080805
  EX_dxylnt_e : 0.000199
  DM_5drib_c : 0.000100
  DM_4crsol_c : 0.000100

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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