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 : forcoa_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (60 of 80: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 37
  Gene deletion: b3399 b4382 b1241 b0351 b4069 b4384 b2744 b3708 b2297 b2458 b0160 b3124 b1982 b2797 b3117 b1814 b4471 b3616 b3589 b0675 b2361 b2291 b0261 b2406 b0112 b2789 b3127 b2943 b0452 b2975 b0114 b3603 b2366 b2492 b0904 b1533 b0514   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.506985 (mmol/gDw/h)
  Minimum Production Rate : 0.199775 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 26.007013
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.874383
  EX_pi_e : 1.088366
  EX_so4_e : 0.327444
  EX_k_e : 0.098960
  EX_fe2_e : 0.008143
  EX_mg2_e : 0.004398
  EX_ca2_e : 0.002639
  EX_cl_e : 0.002639
  EX_cu2_e : 0.000359
  EX_mn2_e : 0.000350
  EX_zn2_e : 0.000173
  EX_ni2_e : 0.000164
  EX_cobalt2_e : 0.000013

Product: (mmol/gDw/h)
  EX_h2o_e : 44.572776
  EX_co2_e : 27.188078
  EX_h_e : 9.061445
  EX_ac_e : 3.802609
  Auxiliary production reaction : 0.199775
  DM_oxam_c : 0.000567
  DM_5drib_c : 0.000340
  DM_4crsol_c : 0.000113

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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