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 : duri_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (46 of 50: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 43
  Gene deletion: b4467 b4069 b4384 b3708 b0910 b3926 b2297 b2458 b2925 b2097 b0030 b2407 b1004 b3713 b1109 b0046 b3236 b2690 b2797 b3117 b1814 b4471 b2440 b3665 b3945 b1602 b4381 b2406 b3654 b3714 b3664 b0114 b0529 b1539 b2492 b0904 b1533 b3927 b1380 b2660 b3662 b1518 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.391358 (mmol/gDw/h)
  Minimum Production Rate : 0.498824 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 991.273508
  EX_o2_e : 280.855140
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.224279
  EX_pi_e : 0.377506
  EX_so4_e : 0.098552
  EX_k_e : 0.076390
  EX_mg2_e : 0.003395
  EX_ca2_e : 0.002037
  EX_cl_e : 0.002037
  EX_cu2_e : 0.000277
  EX_mn2_e : 0.000270
  EX_zn2_e : 0.000133
  EX_ni2_e : 0.000126

Product: (mmol/gDw/h)
  EX_fe3_e : 999.993714
  EX_h2o_e : 544.517532
  EX_co2_e : 31.193053
  EX_ac_e : 4.126607
  Auxiliary production reaction : 0.498824
  DM_mththf_c : 0.000175
  DM_5drib_c : 0.000088
  DM_4crsol_c : 0.000087

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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