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 : ddca_p
List of minimal gene deletion strategies (Download)

Gene deletion strategy (51 of 76: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 25
  Gene deletion: b2836 b0474 b2518 b2744 b4152 b2781 b3844 b1612 b1611 b4122 b2029 b1759 b4374 b4161 b0675 b2361 b2291 b4138 b4123 b0621 b0529 b2197 b3918 b4042 b1206   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.442645 (mmol/gDw/h)
  Minimum Production Rate : 0.467490 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 983.759598
  EX_o2_e : 260.242175
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.408328
  EX_pi_e : 0.426978
  EX_so4_e : 0.111467
  EX_k_e : 0.086401
  EX_mg2_e : 0.003840
  EX_cl_e : 0.002304
  EX_ca2_e : 0.002304
  EX_cu2_e : 0.000314
  EX_mn2_e : 0.000306
  EX_zn2_e : 0.000151
  EX_ni2_e : 0.000143
  EX_cobalt2_e : 0.000011

Product: (mmol/gDw/h)
  EX_fe3_e : 999.992891
  EX_h2o_e : 526.540934
  EX_co2_e : 12.824371
  EX_ac_e : 10.147631
  Auxiliary production reaction : 0.467490
  EX_succ_e : 0.461587
  EX_ura_e : 0.313901
  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.

Last updated: 21-Sep-2023
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