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 : ppcoa_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (82 of 117: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 35
  Gene deletion: b3399 b4069 b2502 b2744 b3708 b3008 b0512 b3115 b1849 b2296 b3236 b2388 b1982 b0394 b2797 b3117 b1814 b4471 b4374 b0675 b2361 b2291 b0261 b0114 b0886 b1539 b2492 b0904 b0591 b2578 b1533 b3927 b3821 b4141 b1798   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.701186 (mmol/gDw/h)
  Minimum Production Rate : 0.177041 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 24.006342
  EX_glc__D_e : 10.000000
  EX_nh4_e : 8.822982
  EX_pi_e : 1.207490
  EX_so4_e : 0.353613
  EX_k_e : 0.136867
  EX_fe2_e : 0.011262
  EX_mg2_e : 0.006083
  EX_ca2_e : 0.003650
  EX_cl_e : 0.003650
  EX_cu2_e : 0.000497
  EX_mn2_e : 0.000485
  EX_zn2_e : 0.000239
  EX_ni2_e : 0.000226
  EX_cobalt2_e : 0.000018

Product: (mmol/gDw/h)
  EX_h2o_e : 47.846310
  EX_co2_e : 25.764098
  EX_h_e : 7.570108
  EX_ac_e : 0.585261
  Auxiliary production reaction : 0.177041
  EX_alltn_e : 0.002737
  DM_5drib_c : 0.002423
  DM_4crsol_c : 0.002109

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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