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 : ppcoa_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (62 of 117: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 33
  Gene deletion: b3553 b3399 b1241 b0351 b4069 b2744 b3708 b0910 b2297 b2458 b0160 b1982 b2797 b3117 b1814 b4471 b3616 b3589 b1033 b4374 b0675 b2361 b2291 b0261 b0507 b0112 b2943 b0452 b0114 b1539 b2492 b0904 b1533   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.494563 (mmol/gDw/h)
  Minimum Production Rate : 0.243883 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 25.689621
  EX_glc__D_e : 10.000000
  EX_nh4_e : 7.048968
  EX_pi_e : 1.208706
  EX_so4_e : 0.368423
  EX_k_e : 0.096535
  EX_fe2_e : 0.007943
  EX_mg2_e : 0.004290
  EX_cl_e : 0.002574
  EX_ca2_e : 0.002574
  EX_cu2_e : 0.000351
  EX_mn2_e : 0.000342
  EX_zn2_e : 0.000169
  EX_ni2_e : 0.000160
  EX_cobalt2_e : 0.000012

Product: (mmol/gDw/h)
  EX_h2o_e : 45.048763
  EX_co2_e : 27.109967
  EX_h_e : 8.644549
  EX_ac_e : 3.367223
  Auxiliary production reaction : 0.243883
  DM_oxam_c : 0.000553
  DM_5drib_c : 0.000332
  EX_glyclt_e : 0.000331
  DM_4crsol_c : 0.000110

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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