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 : mmcoa__S_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (22 of 85: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 31
  Gene deletion: b2836 b3553 b3399 b1241 b0351 b4069 b2744 b3708 b3115 b1849 b2296 b3617 b0160 b1982 b2797 b3117 b1814 b4471 b1033 b4374 b0675 b2361 b2291 b0261 b0507 b0112 b0114 b2366 b2492 b0904 b1533   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.502175 (mmol/gDw/h)
  Minimum Production Rate : 0.500886 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 990.713447
  EX_o2_e : 270.221148
  EX_glc__D_e : 10.000000
  EX_nh4_e : 8.930210
  EX_pi_e : 1.987059
  EX_so4_e : 0.627344
  EX_k_e : 0.098021
  EX_mg2_e : 0.004356
  EX_ca2_e : 0.002614
  EX_cl_e : 0.002614
  EX_cu2_e : 0.000356
  EX_mn2_e : 0.000347
  EX_zn2_e : 0.000171
  EX_ni2_e : 0.000162
  EX_cobalt2_e : 0.000013

Product: (mmol/gDw/h)
  EX_fe3_e : 999.991935
  EX_h2o_e : 545.321108
  EX_co2_e : 21.544360
  EX_ac_e : 2.659300
  Auxiliary production reaction : 0.500886
  DM_oxam_c : 0.000562
  DM_5drib_c : 0.000337
  EX_glyclt_e : 0.000336
  DM_4crsol_c : 0.000112

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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