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 : nac_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (73 of 78: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 35
  Gene deletion: b0474 b2518 b1241 b0351 b3073 b2744 b0910 b4152 b0871 b2297 b2458 b2925 b2097 b1612 b1611 b4122 b1779 b3946 b0825 b4374 b0675 b1493 b3517 b4015 b0614 b0726 b4388 b4138 b4123 b0621 b2587 b2943 b0452 b1539 b1206   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.598622 (mmol/gDw/h)
  Minimum Production Rate : 0.107872 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 991.041510
  EX_o2_e : 277.877552
  EX_glc__D_e : 10.000000
  EX_nh4_e : 7.206215
  EX_pi_e : 0.577434
  EX_so4_e : 0.150745
  EX_k_e : 0.116847
  EX_mg2_e : 0.005193
  EX_ca2_e : 0.003116
  EX_cl_e : 0.003116
  EX_cu2_e : 0.000424
  EX_mn2_e : 0.000414
  EX_zn2_e : 0.000204
  EX_ni2_e : 0.000193
  EX_cobalt2_e : 0.000015

Product: (mmol/gDw/h)
  EX_fe3_e : 999.990386
  EX_h2o_e : 546.867512
  EX_co2_e : 28.315243
  EX_ac_e : 1.346328
  EX_succ_e : 0.626575
  EX_ura_e : 0.316640
  Auxiliary production reaction : 0.107872
  DM_mththf_c : 0.000268
  DM_5drib_c : 0.000135
  DM_4crsol_c : 0.000133

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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