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 : udpglcur_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (57 of 75: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 25
  Gene deletion: b4382 b3831 b4384 b3614 b0910 b4152 b2926 b2781 b0030 b1612 b1611 b4122 b0651 b2162 b1759 b3449 b4138 b4123 b0621 b2406 b3918 b0789 b1249 b0494 b1206   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.630547 (mmol/gDw/h)
  Minimum Production Rate : 0.333020 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 992.319809
  EX_o2_e : 276.021352
  EX_glc__D_e : 10.000000
  EX_nh4_e : 7.704162
  EX_pi_e : 1.274271
  EX_so4_e : 0.158784
  EX_k_e : 0.123078
  EX_mg2_e : 0.005470
  EX_ca2_e : 0.003282
  EX_cl_e : 0.003282
  EX_cu2_e : 0.000447
  EX_mn2_e : 0.000436
  EX_zn2_e : 0.000215
  EX_ni2_e : 0.000204
  EX_cobalt2_e : 0.000016

Product: (mmol/gDw/h)
  EX_fe3_e : 999.989873
  EX_h2o_e : 547.241314
  EX_co2_e : 26.036972
  EX_succ_e : 0.657530
  Auxiliary production reaction : 0.333020
  EX_ura_e : 0.114131
  DM_5drib_c : 0.000142
  DM_4crsol_c : 0.000141

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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