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 : udpg_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (68 of 83: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 27
  Gene deletion: b3831 b2744 b3614 b0910 b4152 b2779 b2781 b0030 b3844 b1612 b1611 b4122 b0651 b2162 b1759 b4374 b2361 b2291 b0411 b4138 b4123 b0621 b0452 b3918 b4042 b1206 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.544438 (mmol/gDw/h)
  Minimum Production Rate : 0.287454 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 30.377206
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.652054
  EX_pi_e : 1.100076
  EX_so4_e : 0.137100
  EX_k_e : 0.106270
  EX_fe2_e : 0.008744
  EX_mg2_e : 0.004723
  EX_ca2_e : 0.002834
  EX_cl_e : 0.002834
  EX_cu2_e : 0.000386
  EX_mn2_e : 0.000376
  EX_zn2_e : 0.000186
  EX_ni2_e : 0.000176
  EX_cobalt2_e : 0.000014

Product: (mmol/gDw/h)
  EX_h2o_e : 48.701130
  EX_co2_e : 30.676050
  EX_h_e : 6.335246
  EX_succ_e : 0.567735
  Auxiliary production reaction : 0.287454
  EX_ura_e : 0.098633
  DM_5drib_c : 0.000122
  DM_4crsol_c : 0.000121

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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