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 : cdpdodec11eg_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (57 of 80: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 25
  Gene deletion: b1054 b4382 b3831 b4384 b3614 b0910 b4152 b2781 b0030 b1612 b1611 b4122 b0651 b2162 b1759 b4138 b4123 b0621 b2406 b2197 b2835 b3918 b1912 b0494 b1206   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.550885 (mmol/gDw/h)
  Minimum Production Rate : 0.290947 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 15.914458
  EX_glc__D_e : 10.000000
  EX_nh4_e : 7.021782
  EX_pi_e : 1.113282
  EX_so4_e : 0.138724
  EX_k_e : 0.107529
  EX_fe2_e : 0.008848
  EX_mg2_e : 0.004779
  EX_cl_e : 0.002867
  EX_ca2_e : 0.002867
  EX_cu2_e : 0.000391
  EX_mn2_e : 0.000381
  EX_zn2_e : 0.000188
  EX_ni2_e : 0.000178
  EX_cobalt2_e : 0.000014

Product: (mmol/gDw/h)
  EX_h2o_e : 40.129221
  EX_co2_e : 20.726525
  EX_h_e : 6.701044
  EX_succ_e : 0.574459
  Auxiliary production reaction : 0.290947
  EX_ura_e : 0.099712
  DM_5drib_c : 0.000124
  DM_4crsol_c : 0.000123

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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