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 : hemeO_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (57 of 98: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 37
  Gene deletion: b4467 b2242 b3831 b3614 b0910 b3752 b2925 b2097 b2781 b1004 b3713 b1109 b0046 b3236 b1612 b1611 b4122 b0907 b1779 b2690 b1759 b1415 b4015 b0411 b3945 b4138 b4123 b0621 b4381 b2492 b0904 b3825 b3028 b3918 b4042 b1206 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.408715 (mmol/gDw/h)
  Minimum Production Rate : 0.035977 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 991.212623
  EX_o2_e : 281.318973
  EX_glc__D_e : 10.000000
  EX_nh4_e : 4.921817
  EX_pi_e : 0.394249
  EX_so4_e : 0.102923
  EX_k_e : 0.079778
  EX_mg2_e : 0.003546
  EX_ca2_e : 0.002127
  EX_cl_e : 0.002127
  EX_cu2_e : 0.000290
  EX_mn2_e : 0.000282
  EX_zn2_e : 0.000139
  EX_ni2_e : 0.000132
  EX_cobalt2_e : 0.000010

Product: (mmol/gDw/h)
  EX_fe3_e : 999.957459
  EX_h2o_e : 545.064483
  EX_co2_e : 32.057538
  EX_ac_e : 3.485170
  EX_succ_e : 0.426205
  EX_ura_e : 0.181909
  Auxiliary production reaction : 0.035977
  EX_dxylnt_e : 0.000182
  DM_5drib_c : 0.000092
  DM_4crsol_c : 0.000091

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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