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 : uri_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (63 of 74: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 25
  Gene deletion: b4382 b0474 b2518 b3831 b4384 b1278 b4152 b2781 b0030 b1612 b1611 b4122 b0651 b2162 b1759 b4161 b0411 b4138 b4123 b0621 b3453 b2835 b3918 b2240 b1206   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.740851 (mmol/gDw/h)
  Minimum Production Rate : 0.391277 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 990.585008
  EX_o2_e : 272.033729
  EX_glc__D_e : 10.000000
  EX_nh4_e : 9.051879
  EX_pi_e : 0.714630
  EX_so4_e : 0.186561
  EX_k_e : 0.144609
  EX_mg2_e : 0.006427
  EX_ca2_e : 0.003856
  EX_cl_e : 0.003856
  EX_cu2_e : 0.000525
  EX_mn2_e : 0.000512
  EX_zn2_e : 0.000253
  EX_ni2_e : 0.000239
  EX_cobalt2_e : 0.000019

Product: (mmol/gDw/h)
  EX_fe3_e : 999.988101
  EX_h2o_e : 545.791944
  EX_co2_e : 22.443359
  EX_succ_e : 0.772554
  Auxiliary production reaction : 0.391277
  EX_ura_e : 0.134096
  DM_5drib_c : 0.000167
  DM_4crsol_c : 0.000165

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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