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 : 12ppd__R_e
List of minimal gene deletion strategies (Download)

Gene deletion strategy (66 of 81: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 28
  Gene deletion: b4467 b1241 b0351 b4384 b2744 b3926 b0871 b2779 b2407 b1004 b3713 b1109 b0046 b3236 b4374 b2361 b2291 b1602 b2913 b3915 b0452 b0529 b2492 b0904 b1380 b0606 b2285 b4209   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.504905 (mmol/gDw/h)
  Minimum Production Rate : 0.066582 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 995.352625
  EX_o2_e : 287.930153
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.452927
  EX_pi_e : 0.487034
  EX_so4_e : 0.127145
  EX_k_e : 0.098554
  EX_mg2_e : 0.004380
  EX_ca2_e : 0.002628
  EX_cl_e : 0.002628
  EX_cu2_e : 0.000358
  EX_mn2_e : 0.000349
  EX_zn2_e : 0.000172
  EX_ni2_e : 0.000163
  EX_cobalt2_e : 0.000013

Product: (mmol/gDw/h)
  EX_fe3_e : 999.991891
  EX_h2o_e : 552.338738
  EX_co2_e : 39.076239
  EX_12ppd__R_e : 0.066582
  DM_5drib_c : 0.000114
  DM_4crsol_c : 0.000113

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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