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 : 4ppan_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (19 of 88: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 31
  Gene deletion: b4382 b1241 b0351 b4069 b4384 b3708 b3752 b2930 b4232 b3697 b3925 b3115 b1849 b2296 b3617 b2407 b2690 b1982 b2797 b3117 b1814 b4471 b0261 b3945 b2406 b0114 b2366 b2492 b0904 b1533 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.447861 (mmol/gDw/h)
  Minimum Production Rate : 1.024361 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 26.853635
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.493337
  EX_pi_e : 1.456371
  EX_so4_e : 0.112780
  EX_k_e : 0.087419
  EX_fe2_e : 0.007193
  EX_mg2_e : 0.003885
  EX_ca2_e : 0.002331
  EX_cl_e : 0.002331
  EX_cu2_e : 0.000318
  EX_mn2_e : 0.000309
  EX_zn2_e : 0.000153
  EX_ni2_e : 0.000145
  EX_cobalt2_e : 0.000011

Product: (mmol/gDw/h)
  EX_h2o_e : 44.918221
  EX_co2_e : 28.438328
  EX_h_e : 7.985840
  EX_ac_e : 1.189375
  Auxiliary production reaction : 1.024361
  EX_ins_e : 0.157904
  DM_oxam_c : 0.000501
  DM_5drib_c : 0.000301
  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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