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 : 2dr1p_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (36 of 40: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 31
  Gene deletion: b4467 b4069 b4384 b3752 b3926 b2297 b2458 b2407 b3844 b1004 b3713 b1109 b0046 b3236 b1612 b1611 b4122 b1779 b0937 b1602 b4381 b0114 b0529 b2492 b0904 b1380 b2660 b1771 b1518 b0606 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.430246 (mmol/gDw/h)
  Minimum Production Rate : 0.472332 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 35.559520
  EX_glc__D_e : 10.000000
  EX_nh4_e : 4.646616
  EX_pi_e : 0.887350
  EX_so4_e : 0.108344
  EX_k_e : 0.083981
  EX_fe2_e : 0.006910
  EX_mg2_e : 0.003732
  EX_cl_e : 0.002239
  EX_ca2_e : 0.002239
  EX_cu2_e : 0.000305
  EX_mn2_e : 0.000297
  EX_zn2_e : 0.000147
  EX_ni2_e : 0.000139
  EX_cobalt2_e : 0.000011

Product: (mmol/gDw/h)
  EX_h2o_e : 48.996424
  EX_co2_e : 36.265183
  EX_h_e : 5.573396
  Auxiliary production reaction : 0.472332
  EX_3hpp_e : 0.472332
  EX_fum_e : 0.448657
  EX_ac_e : 0.250483
  DM_mththf_c : 0.000193
  DM_5drib_c : 0.000097
  DM_4crsol_c : 0.000096

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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