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 : ins_e
List of minimal gene deletion strategies (Download)

Gene deletion strategy (101 of 109: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 41
  Gene deletion: b4269 b3942 b1732 b0493 b3588 b3003 b3011 b0474 b2518 b1241 b0351 b4384 b2744 b1479 b3752 b0871 b2926 b2407 b3236 b2463 b3616 b3589 b2210 b3665 b4374 b2361 b2291 b3551 b4219 b1832 b1778 b0114 b0529 b2492 b0904 b1710 b2480 b1517 b0606 b2285 b4209   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.365861 (mmol/gDw/h)
  Minimum Production Rate : 0.594908 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 34.515554
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.332128
  EX_pi_e : 0.352911
  EX_so4_e : 0.092131
  EX_k_e : 0.071413
  EX_mg2_e : 0.003174
  EX_fe2_e : 0.003019
  EX_fe3_e : 0.002857
  EX_ca2_e : 0.001904
  EX_cl_e : 0.001904
  EX_cu2_e : 0.000259
  EX_mn2_e : 0.000253
  EX_zn2_e : 0.000125
  EX_ni2_e : 0.000118

Product: (mmol/gDw/h)
  EX_h2o_e : 49.879037
  EX_co2_e : 33.290635
  EX_h_e : 7.699229
  EX_mal__L_e : 0.976917
  EX_acald_e : 0.916831
  EX_ins_e : 0.594908
  EX_ade_e : 0.000246
  EX_mththf_e : 0.000164
  DM_5drib_c : 0.000082
  DM_4crsol_c : 0.000082

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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