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 : 12ppd__S_e
List of minimal gene deletion strategies (Download)

Gene deletion strategy (26 of 92: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 28
  Gene deletion: b4467 b1241 b0351 b4069 b2297 b2458 b2779 b1004 b3713 b1109 b0046 b3236 b3945 b1602 b2913 b4381 b3915 b1727 b0529 b2492 b0904 b1380 b1517 b0606 b0221 b2285 b1007 b4209   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.461847 (mmol/gDw/h)
  Minimum Production Rate : 0.321420 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 995.480068
  EX_o2_e : 284.840482
  EX_glc__D_e : 10.000000
  EX_nh4_e : 4.987907
  EX_pi_e : 0.445500
  EX_so4_e : 0.116302
  EX_k_e : 0.090149
  EX_mg2_e : 0.004007
  EX_ca2_e : 0.002404
  EX_cl_e : 0.002404
  EX_cu2_e : 0.000327
  EX_mn2_e : 0.000319
  EX_zn2_e : 0.000157
  EX_ni2_e : 0.000149
  EX_cobalt2_e : 0.000012

Product: (mmol/gDw/h)
  EX_fe3_e : 999.992582
  EX_h2o_e : 548.020318
  EX_co2_e : 37.279649
  EX_etoh_e : 1.130301
  EX_12ppd__S_e : 0.321420
  EX_ac_e : 0.268881
  DM_mththf_c : 0.000207
  DM_5drib_c : 0.000104
  DM_4crsol_c : 0.000103

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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