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 : succoa_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (22 of 28: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 49
  Gene deletion: b2836 b3553 b1478 b3399 b4382 b1241 b0351 b4069 b4384 b2744 b3708 b3115 b1849 b2296 b2779 b0030 b3844 b1004 b3713 b1109 b0046 b3236 b1982 b2797 b3117 b1814 b4471 b1033 b1623 b0261 b2799 b3945 b1602 b0507 b0153 b2913 b4381 b0590 b2406 b1539 b2492 b0904 b1533 b1380 b4141 b1798 b0606 b2285 b1011   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.406298 (mmol/gDw/h)
  Minimum Production Rate : 0.047523 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 36.938614
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.869311
  EX_pi_e : 0.534486
  EX_so4_e : 0.149837
  EX_k_e : 0.079307
  EX_fe2_e : 0.006526
  EX_mg2_e : 0.003525
  EX_ca2_e : 0.002115
  EX_cl_e : 0.002115
  EX_cu2_e : 0.000288
  EX_mn2_e : 0.000281
  EX_zn2_e : 0.000139
  EX_ni2_e : 0.000131
  EX_cobalt2_e : 0.000010

Product: (mmol/gDw/h)
  EX_h2o_e : 52.779705
  EX_co2_e : 36.218583
  EX_h_e : 7.687238
  EX_ac_e : 1.615252
  EX_xan_e : 0.536598
  Auxiliary production reaction : 0.047523
  EX_ade_e : 0.000455
  DM_5drib_c : 0.000273
  DM_4crsol_c : 0.000091

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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