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 : cdpdtdecg_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (62 of 73: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 25
  Gene deletion: b4382 b0474 b2518 b3831 b4384 b1278 b4152 b2781 b0030 b1612 b1611 b4122 b0651 b2162 b1759 b4161 b1701 b1805 b4138 b4123 b0621 b2406 b2197 b3918 b1206   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.578199 (mmol/gDw/h)
  Minimum Production Rate : 0.305373 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 992.957421
  EX_o2_e : 267.085412
  EX_glc__D_e : 10.000000
  EX_nh4_e : 7.369933
  EX_pi_e : 1.168480
  EX_so4_e : 0.145602
  EX_k_e : 0.112860
  EX_mg2_e : 0.005016
  EX_ca2_e : 0.003010
  EX_cl_e : 0.003010
  EX_cu2_e : 0.000410
  EX_mn2_e : 0.000400
  EX_zn2_e : 0.000197
  EX_ni2_e : 0.000187
  EX_cobalt2_e : 0.000014

Product: (mmol/gDw/h)
  EX_fe3_e : 999.990714
  EX_h2o_e : 540.971593
  EX_co2_e : 21.222271
  EX_succ_e : 0.602941
  Auxiliary production reaction : 0.305373
  EX_ura_e : 0.104656
  DM_5drib_c : 0.000130
  DM_4crsol_c : 0.000129

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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