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 : didp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (60 of 87: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 29
  Gene deletion: b3399 b0474 b2518 b1241 b0351 b4069 b2744 b0871 b2297 b2458 b2925 b2097 b3236 b1779 b3616 b3589 b3946 b2210 b0825 b0675 b2361 b4381 b0114 b0529 b2492 b0904 b0515 b1518 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.313362 (mmol/gDw/h)
  Minimum Production Rate : 0.400507 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 30.113684
  EX_glc__D_e : 10.000000
  EX_nh4_e : 4.987158
  EX_pi_e : 1.103285
  EX_so4_e : 0.078911
  EX_k_e : 0.061166
  EX_fe2_e : 0.005033
  EX_mg2_e : 0.002718
  EX_cl_e : 0.001631
  EX_ca2_e : 0.001631
  EX_cu2_e : 0.000222
  EX_mn2_e : 0.000217
  EX_zn2_e : 0.000107
  EX_ni2_e : 0.000101

Product: (mmol/gDw/h)
  EX_h2o_e : 45.349991
  EX_co2_e : 27.694119
  EX_h_e : 9.513614
  EX_pyr_e : 4.573280
  EX_ac_e : 0.858671
  Auxiliary production reaction : 0.400507
  EX_alltn_e : 0.000211
  DM_mththf_c : 0.000140
  DM_5drib_c : 0.000071
  DM_4crsol_c : 0.000070

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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