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 : cdigmp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (78 of 79: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 47
  Gene deletion: b3553 b1478 b3399 b1241 b4069 b2502 b2744 b3115 b1849 b2296 b2925 b2097 b1238 b1004 b3713 b1109 b0046 b3236 b1638 b2690 b0207 b3012 b1982 b4139 b1033 b0675 b2361 b0261 b2799 b1602 b4381 b3915 b0114 b0755 b3612 b0529 b2492 b0904 b1781 b3001 b3927 b3029 b1380 b0325 b2660 b1771 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.391244 (mmol/gDw/h)
  Minimum Production Rate : 0.033573 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 32.220157
  EX_glc__D_e : 10.000000
  EX_nh4_e : 4.561135
  EX_pi_e : 0.444543
  EX_so4_e : 0.098523
  EX_k_e : 0.076368
  EX_fe3_e : 0.006284
  EX_mg2_e : 0.003394
  EX_ca2_e : 0.002036
  EX_cl_e : 0.002036
  EX_cu2_e : 0.000277
  EX_mn2_e : 0.000270
  EX_zn2_e : 0.000133
  EX_ni2_e : 0.000126

Product: (mmol/gDw/h)
  EX_h2o_e : 44.056735
  EX_co2_e : 32.855299
  EX_h_e : 9.076572
  EX_ac_e : 5.206796
  Auxiliary production reaction : 0.033573
  DM_5drib_c : 0.000263
  DM_4crsol_c : 0.000087

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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