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 : dcmp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (105 of 117: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 44
  Gene deletion: b3399 b4069 b2502 b2744 b3708 b3008 b2297 b2458 b2779 b1238 b3236 b1779 b1982 b2797 b3117 b1814 b4471 b0596 b0675 b2361 b0261 b2342 b3845 b3709 b4381 b2406 b3161 b0112 b2789 b3127 b0452 b2975 b0114 b3603 b0886 b2366 b2492 b0904 b2578 b1533 b3927 b1473 b4141 b1798   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.605754 (mmol/gDw/h)
  Minimum Production Rate : 0.766414 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 26.978885
  EX_glc__D_e : 10.000000
  EX_nh4_e : 8.850601
  EX_pi_e : 1.353488
  EX_so4_e : 0.152541
  EX_k_e : 0.118239
  EX_fe2_e : 0.009729
  EX_mg2_e : 0.005255
  EX_ca2_e : 0.003153
  EX_cl_e : 0.003153
  EX_cu2_e : 0.000429
  EX_mn2_e : 0.000419
  EX_zn2_e : 0.000207
  EX_ni2_e : 0.000196
  EX_cobalt2_e : 0.000015

Product: (mmol/gDw/h)
  EX_h2o_e : 49.654252
  EX_co2_e : 27.501675
  EX_h_e : 8.228065
  Auxiliary production reaction : 0.769174
  EX_ac_e : 0.352662
  DM_oxam_c : 0.000985
  DM_5drib_c : 0.000714
  DM_4crsol_c : 0.000442

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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