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 : 12ppd__S_e
List of minimal gene deletion strategies (Download)

Gene deletion strategy (51 of 92: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 32
  Gene deletion: b4467 b1241 b0351 b2930 b4232 b3697 b3925 b0871 b2926 b1004 b3713 b1109 b0046 b3236 b1638 b2690 b4139 b1493 b3517 b4015 b3945 b1602 b2913 b4381 b1727 b2492 b0904 b1298 b3029 b1380 b1695 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.417812 (mmol/gDw/h)
  Minimum Production Rate : 1.936967 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 34.204550
  EX_glc__D_e : 10.000000
  EX_nh4_e : 4.512331
  EX_pi_e : 0.403024
  EX_so4_e : 0.105213
  EX_k_e : 0.081554
  EX_fe2_e : 0.006710
  EX_mg2_e : 0.003625
  EX_ca2_e : 0.002175
  EX_cl_e : 0.002175
  EX_cu2_e : 0.000296
  EX_mn2_e : 0.000289
  EX_zn2_e : 0.000142
  EX_ni2_e : 0.000135
  EX_cobalt2_e : 0.000010

Product: (mmol/gDw/h)
  EX_h2o_e : 46.129421
  EX_co2_e : 37.034814
  EX_h_e : 3.839021
  EX_12ppd__S_e : 1.938645
  DM_5drib_c : 0.000094
  DM_4crsol_c : 0.000093

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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