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 (62 of 83: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 25
  Gene deletion: b0474 b2518 b3831 b3752 b4152 b2781 b1612 b1611 b4122 b1759 b4161 b4138 b4123 b0621 b4381 b2406 b0452 b0114 b0755 b3612 b3825 b3918 b4042 b1813 b1206   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.649517 (mmol/gDw/h)
  Minimum Production Rate : 0.342987 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 992.431685
  EX_o2_e : 274.656642
  EX_glc__D_e : 10.000000
  EX_nh4_e : 7.935941
  EX_pi_e : 1.312503
  EX_so4_e : 0.163561
  EX_k_e : 0.126781
  EX_mg2_e : 0.005635
  EX_ca2_e : 0.003381
  EX_cl_e : 0.003381
  EX_cu2_e : 0.000461
  EX_mn2_e : 0.000449
  EX_zn2_e : 0.000221
  EX_ni2_e : 0.000210
  EX_cobalt2_e : 0.000016

Product: (mmol/gDw/h)
  EX_fe3_e : 999.989568
  EX_h2o_e : 546.514796
  EX_co2_e : 25.015772
  EX_succ_e : 0.677312
  Auxiliary production reaction : 0.342987
  EX_ura_e : 0.117617
  DM_5drib_c : 0.000146
  DM_4crsol_c : 0.000145

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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