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 (23 of 88: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 32
  Gene deletion: b4382 b1241 b0351 b4069 b4384 b3708 b0871 b3115 b1849 b2296 b2779 b2925 b2097 b3617 b0030 b2407 b2690 b1982 b2797 b3117 b1814 b4471 b3665 b3945 b2913 b2406 b0114 b2366 b2492 b0904 b1533 b1517   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.526050 (mmol/gDw/h)
  Minimum Production Rate : 0.329835 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 990.172530
  EX_o2_e : 275.646045
  EX_glc__D_e : 10.000000
  EX_nh4_e : 8.502928
  EX_pi_e : 0.837267
  EX_so4_e : 0.132470
  EX_k_e : 0.102681
  EX_mg2_e : 0.004563
  EX_ca2_e : 0.002738
  EX_cl_e : 0.002738
  EX_cu2_e : 0.000373
  EX_mn2_e : 0.000364
  EX_zn2_e : 0.000179
  EX_ni2_e : 0.000170
  EX_cobalt2_e : 0.000013

Product: (mmol/gDw/h)
  EX_fe3_e : 999.991551
  EX_h2o_e : 546.648772
  EX_co2_e : 25.543357
  EX_ac_e : 1.833820
  EX_ins_e : 0.622506
  Auxiliary production reaction : 0.329835
  EX_ade_e : 0.000354
  DM_mththf_c : 0.000236
  EX_glyc__R_e : 0.000176
  DM_5drib_c : 0.000118
  DM_4crsol_c : 0.000117

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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