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 : dctp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (68 of 73: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 46
  Gene deletion: b3399 b3942 b1732 b1241 b0351 b4069 b2502 b4384 b2744 b3708 b1479 b0910 b3115 b1849 b2296 b3617 b3236 b2463 b1982 b2797 b3117 b1814 b4471 b2210 b3665 b4374 b0675 b2361 b2291 b3551 b4219 b1832 b1778 b0114 b2366 b2492 b0904 b1533 b2835 b1710 b2480 b1511 b1206 b0606 b2285 b4209   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.413962 (mmol/gDw/h)
  Minimum Production Rate : 1.239286 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 993.131345
  EX_o2_e : 279.004659
  EX_glc__D_e : 10.000000
  EX_nh4_e : 8.190005
  EX_pi_e : 4.117169
  EX_so4_e : 0.104244
  EX_k_e : 0.080802
  EX_mg2_e : 0.003591
  EX_cl_e : 0.002155
  EX_ca2_e : 0.002155
  EX_cu2_e : 0.000293
  EX_mn2_e : 0.000286
  EX_zn2_e : 0.000141
  EX_ni2_e : 0.000134
  EX_cobalt2_e : 0.000010

Product: (mmol/gDw/h)
  EX_fe3_e : 999.993351
  EX_h2o_e : 552.405889
  EX_co2_e : 28.217508
  Auxiliary production reaction : 1.239286
  EX_ac_e : 0.953213
  EX_fum_e : 0.432233
  EX_ade_e : 0.000279
  EX_mththf_e : 0.000185
  DM_5drib_c : 0.000093
  DM_4crsol_c : 0.000092

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.

Last updated: 21-Sep-2023
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