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 : dtdpglu_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (54 of 74: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 25
  Gene deletion: b2836 b3831 b2744 b3614 b0910 b3752 b4152 b2926 b2781 b1612 b1611 b4122 b1759 b4374 b2361 b2291 b4138 b4123 b0621 b2406 b0529 b2197 b3918 b1912 b1206   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.611001 (mmol/gDw/h)
  Minimum Production Rate : 0.322648 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 992.880487
  EX_o2_e : 276.107212
  EX_glc__D_e : 10.000000
  EX_nh4_e : 7.465339
  EX_pi_e : 1.234671
  EX_so4_e : 0.153862
  EX_k_e : 0.119263
  EX_mg2_e : 0.005300
  EX_cl_e : 0.003180
  EX_ca2_e : 0.003180
  EX_cu2_e : 0.000433
  EX_mn2_e : 0.000422
  EX_zn2_e : 0.000208
  EX_ni2_e : 0.000197
  EX_cobalt2_e : 0.000015

Product: (mmol/gDw/h)
  EX_fe3_e : 999.990187
  EX_h2o_e : 546.991823
  EX_co2_e : 26.767693
  EX_succ_e : 0.637147
  Auxiliary production reaction : 0.322648
  EX_ura_e : 0.110642
  DM_5drib_c : 0.000137
  DM_4crsol_c : 0.000136

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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