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 : 6hmhptpp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (54 of 95: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 28
  Gene deletion: b3399 b1241 b0351 b4069 b2502 b2744 b2297 b2458 b2779 b3617 b1982 b4374 b0675 b2361 b2291 b0261 b0112 b2789 b3127 b2975 b0114 b3603 b0755 b3612 b0529 b2492 b0904 b0514   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.408998 (mmol/gDw/h)
  Minimum Production Rate : 1.567669 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 27.816364
  EX_nh4_e : 12.255952
  EX_glc__D_e : 10.000000
  EX_pi_e : 3.529861
  EX_so4_e : 0.102994
  EX_k_e : 0.079834
  EX_fe2_e : 0.006569
  EX_mg2_e : 0.003548
  EX_ca2_e : 0.002129
  EX_cl_e : 0.002129
  EX_cu2_e : 0.000290
  EX_mn2_e : 0.000283
  EX_zn2_e : 0.000139
  EX_ni2_e : 0.000132
  EX_cobalt2_e : 0.000010

Product: (mmol/gDw/h)
  EX_h2o_e : 54.382870
  EX_co2_e : 24.769407
  EX_h_e : 13.763421
  EX_ac_e : 3.733788
  Auxiliary production reaction : 1.567669
  DM_oxam_c : 0.000458
  DM_5drib_c : 0.000274
  DM_4crsol_c : 0.000091

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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