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 (49 of 98: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 29
  Gene deletion: b1478 b4382 b0474 b2518 b1241 b4384 b2744 b4152 b2925 b2097 b2781 b1612 b1611 b4122 b1779 b2690 b1759 b4374 b4161 b0675 b0822 b4138 b4123 b0621 b2913 b3821 b3918 b4042 b1206   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.615241 (mmol/gDw/h)
  Minimum Production Rate : 0.026537 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 991.935980
  EX_o2_e : 277.064555
  EX_glc__D_e : 10.000000
  EX_nh4_e : 7.353599
  EX_pi_e : 0.593465
  EX_so4_e : 0.154930
  EX_k_e : 0.120091
  EX_mg2_e : 0.005337
  EX_ca2_e : 0.003202
  EX_cl_e : 0.003202
  EX_cu2_e : 0.000436
  EX_mn2_e : 0.000425
  EX_zn2_e : 0.000210
  EX_ni2_e : 0.000199
  EX_cobalt2_e : 0.000015

Product: (mmol/gDw/h)
  EX_fe3_e : 999.908344
  EX_h2o_e : 547.969921
  EX_co2_e : 28.238599
  EX_succ_e : 0.641569
  EX_ura_e : 0.190973
  EX_pheme_e : 0.055237
  Auxiliary production reaction : 0.026537
  DM_5drib_c : 0.000138
  DM_4crsol_c : 0.000137

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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