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 : ncam_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (101 of 116: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 33
  Gene deletion: b4467 b2242 b0474 b2518 b3831 b3752 b2925 b2097 b2781 b1004 b3713 b1109 b0046 b1612 b1611 b4122 b1779 b1759 b3946 b2210 b0825 b4161 b1415 b4138 b4123 b0621 b4381 b2492 b0904 b3028 b3918 b1206 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.439545 (mmol/gDw/h)
  Minimum Production Rate : 0.232143 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 991.672913
  EX_o2_e : 282.456616
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.370450
  EX_pi_e : 0.423987
  EX_so4_e : 0.110686
  EX_k_e : 0.085796
  EX_mg2_e : 0.003813
  EX_ca2_e : 0.002288
  EX_cl_e : 0.002288
  EX_cu2_e : 0.000312
  EX_mn2_e : 0.000304
  EX_zn2_e : 0.000150
  EX_ni2_e : 0.000142
  EX_cobalt2_e : 0.000011

Product: (mmol/gDw/h)
  EX_fe3_e : 999.992940
  EX_h2o_e : 546.784430
  EX_co2_e : 32.931791
  EX_ac_e : 2.741204
  EX_succ_e : 0.458354
  Auxiliary production reaction : 0.232143
  EX_ura_e : 0.079559
  DM_5drib_c : 0.000099
  DM_4crsol_c : 0.000098

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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