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 : rhcys_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (17 of 41: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 30
  Gene deletion: b2836 b4382 b1241 b0351 b4069 b4384 b3708 b2297 b2458 b2925 b2097 b1850 b3617 b0030 b2407 b2687 b1982 b1200 b2797 b3117 b1814 b4471 b2406 b0112 b0114 b1539 b2492 b0904 b1533 b3662   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.506416 (mmol/gDw/h)
  Minimum Production Rate : 0.672420 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 992.485315
  EX_o2_e : 273.681712
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.141669
  EX_so4_e : 0.799946
  EX_pi_e : 0.488492
  EX_k_e : 0.098849
  EX_mg2_e : 0.004393
  EX_cl_e : 0.002636
  EX_ca2_e : 0.002636
  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_fe3_e : 999.991866
  EX_h2o_e : 541.495639
  EX_co2_e : 26.109401
  EX_ac_e : 3.525821
  Auxiliary production reaction : 0.672420
  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.

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Last updated: 21-Sep-2023
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