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 : trp__L_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (100 of 116: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 50
  Gene deletion: b3553 b3399 b4382 b0474 b2518 b1241 b0351 b4069 b4384 b2744 b3708 b2297 b2458 b2926 b0160 b0583 b3962 b1982 b4139 b2797 b3117 b1814 b4471 b3616 b3589 b4267 b1033 b0675 b2361 b2291 b1415 b1014 b0261 b2799 b3945 b0507 b3709 b2406 b3161 b0112 b0114 b1539 b2492 b0904 b1533 b3821 b1380 b2413 b1473 b4266   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.315149 (mmol/gDw/h)
  Minimum Production Rate : 0.339676 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 33.414147
  EX_glc__D_e : 10.000000
  EX_nh4_e : 4.686654
  EX_so4_e : 0.682730
  EX_pi_e : 0.303994
  EX_k_e : 0.061515
  EX_fe2_e : 0.005062
  EX_mg2_e : 0.002734
  EX_ca2_e : 0.001640
  EX_cl_e : 0.001640
  EX_cu2_e : 0.000223
  EX_mn2_e : 0.000218
  EX_zn2_e : 0.000107
  EX_ni2_e : 0.000102

Product: (mmol/gDw/h)
  EX_h2o_e : 48.011436
  EX_co2_e : 35.764378
  EX_h_e : 5.244846
  EX_ac_e : 2.272235
  EX_met__L_e : 0.603369
  Auxiliary production reaction : 0.339676
  DM_oxam_c : 0.000353
  DM_5drib_c : 0.000211
  EX_dxylnt_e : 0.000211
  DM_4crsol_c : 0.000070

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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