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 : udpLa4o_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (66 of 83: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 28
  Gene deletion: b4382 b4384 b2744 b3614 b0910 b4152 b2925 b2097 b2926 b2781 b1612 b1611 b4122 b1759 b3946 b0825 b4374 b0675 b4138 b4123 b0621 b0755 b3612 b0529 b2197 b3918 b1912 b1206   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.603772 (mmol/gDw/h)
  Minimum Production Rate : 0.318879 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 992.216646
  EX_o2_e : 276.314358
  EX_glc__D_e : 10.000000
  EX_nh4_e : 7.377012
  EX_pi_e : 1.220160
  EX_so4_e : 0.152042
  EX_k_e : 0.117852
  EX_mg2_e : 0.005238
  EX_ca2_e : 0.003143
  EX_cl_e : 0.003143
  EX_cu2_e : 0.000428
  EX_mn2_e : 0.000417
  EX_zn2_e : 0.000206
  EX_ni2_e : 0.000195
  EX_cobalt2_e : 0.000015

Product: (mmol/gDw/h)
  EX_fe3_e : 999.990303
  EX_h2o_e : 546.979717
  EX_co2_e : 26.301711
  EX_succ_e : 1.003696
  Auxiliary production reaction : 0.318879
  EX_ura_e : 0.109285
  DM_5drib_c : 0.000136
  DM_4crsol_c : 0.000135

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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