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 : cdpdodecg_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (55 of 77: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 25
  Gene deletion: b2836 b0474 b2518 b2744 b4152 b2781 b1612 b1611 b4122 b1759 b4374 b4161 b0675 b2361 b2291 b2342 b3845 b4138 b4123 b0621 b2197 b3918 b1912 b1206 b3546   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.535738 (mmol/gDw/h)
  Minimum Production Rate : 0.282947 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 993.474605
  EX_o2_e : 266.841546
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.828709
  EX_pi_e : 1.082671
  EX_so4_e : 0.134910
  EX_k_e : 0.104572
  EX_mg2_e : 0.004648
  EX_ca2_e : 0.002789
  EX_cl_e : 0.002789
  EX_cu2_e : 0.000380
  EX_mn2_e : 0.000370
  EX_zn2_e : 0.000183
  EX_ni2_e : 0.000173
  EX_cobalt2_e : 0.000013

Product: (mmol/gDw/h)
  EX_fe3_e : 999.991396
  EX_h2o_e : 540.105396
  EX_co2_e : 21.806398
  EX_succ_e : 0.558663
  Auxiliary production reaction : 0.282947
  EX_ura_e : 0.096970
  DM_5drib_c : 0.000121
  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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