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 : dcdp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (60 of 84: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 41
  Gene deletion: b3553 b3399 b4382 b4069 b2502 b4384 b2744 b0871 b2297 b2458 b2779 b2925 b2097 b3844 b1004 b3713 b1109 b0046 b3236 b1982 b3946 b0825 b1033 b0675 b2361 b0261 b2799 b3945 b1602 b4381 b3915 b1727 b0114 b0529 b2492 b0904 b1380 b2660 b0606 b2285 b1009   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.312128 (mmol/gDw/h)
  Minimum Production Rate : 0.705719 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 29.122159
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.489857
  EX_pi_e : 1.712519
  EX_so4_e : 0.078600
  EX_k_e : 0.060925
  EX_fe3_e : 0.005013
  EX_mg2_e : 0.002708
  EX_ca2_e : 0.001625
  EX_cl_e : 0.001625
  EX_cu2_e : 0.000221
  EX_mn2_e : 0.000216
  EX_zn2_e : 0.000106
  EX_ni2_e : 0.000101

Product: (mmol/gDw/h)
  EX_h2o_e : 45.791367
  EX_co2_e : 27.243060
  EX_h_e : 8.694873
  EX_pyr_e : 4.227005
  Auxiliary production reaction : 0.705719
  EX_etoh_e : 0.273585
  EX_ac_e : 0.181716
  EX_ade_e : 0.000349
  DM_5drib_c : 0.000209
  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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