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 : orot_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (14 of 14: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 56
  Gene deletion: b2242 b3553 b3399 b3942 b1732 b1241 b0351 b4069 b2744 b2297 b2458 b2926 b3617 b0160 b3844 b1612 b1611 b4122 b3962 b0104 b4267 b1033 b0675 b2361 b1415 b3551 b1014 b2799 b3945 b4138 b4123 b0621 b0153 b2913 b4219 b1832 b1778 b4381 b2406 b0112 b4265 b0114 b0584 b0529 b1539 b2492 b0904 b3927 b3028 b1380 b1710 b2480 b4266 b1518 b1206 b0606   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.332234 (mmol/gDw/h)
  Minimum Production Rate : 0.024914 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 35.388726
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.182686
  EX_pi_e : 0.320475
  EX_so4_e : 0.083663
  EX_k_e : 0.064850
  EX_fe2_e : 0.005336
  EX_mg2_e : 0.002882
  EX_ca2_e : 0.001729
  EX_cl_e : 0.001729
  EX_cu2_e : 0.000236
  EX_mn2_e : 0.000230
  EX_zn2_e : 0.000113
  EX_ni2_e : 0.000107

Product: (mmol/gDw/h)
  EX_h2o_e : 49.580069
  EX_co2_e : 33.319736
  EX_h_e : 10.541343
  EX_ac_e : 1.643455
  EX_succ_e : 1.612084
  EX_xan_e : 0.635866
  Auxiliary production reaction : 0.024914
  DM_oxam_c : 0.001297
  EX_dxylnt_e : 0.000222
  EX_mththf_e : 0.000149
  DM_5drib_c : 0.000075
  DM_4crsol_c : 0.000074

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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