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 : g3pg_e
List of minimal gene deletion strategies (Download)

Gene deletion strategy (95 of 110: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 36
  Gene deletion: b4467 b2242 b2744 b3614 b0910 b2779 b2781 b1004 b3713 b1109 b0046 b1612 b1611 b4122 b1759 b3449 b2210 b4374 b0675 b2361 b2291 b1415 b4138 b4123 b0621 b2913 b2239 b2492 b0904 b3028 b3918 b0789 b1249 b1695 b1206 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.448404 (mmol/gDw/h)
  Minimum Production Rate : 0.062341 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 36.025433
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.362374
  EX_pi_e : 0.494874
  EX_so4_e : 0.112917
  EX_k_e : 0.087525
  EX_fe2_e : 0.065362
  EX_mg2_e : 0.003890
  EX_ca2_e : 0.002334
  EX_cl_e : 0.002334
  EX_cu2_e : 0.000318
  EX_mn2_e : 0.000310
  EX_zn2_e : 0.000153
  EX_ni2_e : 0.000145
  EX_cobalt2_e : 0.000011

Product: (mmol/gDw/h)
  EX_h2o_e : 51.163101
  EX_co2_e : 36.799188
  EX_h_e : 5.745250
  EX_succ_e : 0.467592
  EX_ura_e : 0.143503
  EX_g3pg_e : 0.062341
  EX_pheme_e : 0.058161
  DM_5drib_c : 0.000101
  DM_4crsol_c : 0.000100

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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