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 : ac_e
List of minimal gene deletion strategies (Download)

Gene deletion strategy (18 of 18: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 30
  Gene deletion: b3553 b1241 b0351 b3926 b2925 b2097 b1004 b3713 b1109 b0046 b3236 b1779 b2690 b1525 b1033 b2661 b4014 b2976 b3945 b1602 b0507 b2913 b3915 b0452 b1539 b1380 b0606 b2285 b3924 b4209   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.482358 (mmol/gDw/h)
  Minimum Production Rate : 1.719187 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 993.840970
  EX_o2_e : 283.324367
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.209423
  EX_pi_e : 0.465285
  EX_so4_e : 0.121467
  EX_k_e : 0.094153
  EX_mg2_e : 0.004184
  EX_cl_e : 0.002511
  EX_ca2_e : 0.002511
  EX_cu2_e : 0.000342
  EX_mn2_e : 0.000333
  EX_zn2_e : 0.000164
  EX_ni2_e : 0.000156
  EX_cobalt2_e : 0.000012

Product: (mmol/gDw/h)
  EX_fe3_e : 999.992253
  EX_h2o_e : 547.089528
  EX_co2_e : 35.158129
  EX_ac_e : 1.719187
  EX_etoh_e : 0.802463
  DM_5drib_c : 0.000109
  DM_4crsol_c : 0.000108

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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