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 : pe161_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (65 of 81: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 25
  Gene deletion: b3831 b2744 b1278 b3614 b0910 b3752 b4152 b2781 b1612 b1611 b4122 b1759 b4374 b2361 b2291 b1701 b1805 b4138 b4123 b0621 b2406 b2197 b3918 b1206 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.510109 (mmol/gDw/h)
  Minimum Production Rate : 0.269411 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 993.786778
  EX_o2_e : 271.465644
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.502026
  EX_pi_e : 0.761465
  EX_so4_e : 0.128456
  EX_k_e : 0.099570
  EX_mg2_e : 0.004425
  EX_ca2_e : 0.002655
  EX_cl_e : 0.002655
  EX_cu2_e : 0.000362
  EX_mn2_e : 0.000352
  EX_zn2_e : 0.000174
  EX_ni2_e : 0.000165
  EX_cobalt2_e : 0.000013

Product: (mmol/gDw/h)
  EX_fe3_e : 999.991807
  EX_h2o_e : 542.673617
  EX_co2_e : 25.519450
  EX_succ_e : 0.531937
  EX_ura_e : 0.361742
  Auxiliary production reaction : 0.269411
  DM_5drib_c : 0.000115
  DM_4crsol_c : 0.000114

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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