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 : ugmd_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (65 of 75: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 31
  Gene deletion: b0474 b2518 b3831 b4152 b2781 b0030 b3236 b1612 b1611 b4122 b1638 b0651 b2162 b3908 b1656 b1759 b2440 b4161 b4138 b4123 b0621 b2913 b4381 b2406 b0452 b2197 b3918 b1912 b1206 b2285 b3924   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.480167 (mmol/gDw/h)
  Minimum Production Rate : 0.253559 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 28.928440
  EX_glc__D_e : 10.000000
  EX_nh4_e : 7.134622
  EX_pi_e : 0.970291
  EX_so4_e : 0.120916
  EX_k_e : 0.093725
  EX_fe2_e : 0.004605
  EX_mg2_e : 0.004165
  EX_fe3_e : 0.003107
  EX_ca2_e : 0.002499
  EX_cl_e : 0.002499
  EX_cu2_e : 0.000340
  EX_mn2_e : 0.000332
  EX_zn2_e : 0.000164
  EX_ni2_e : 0.000155
  EX_cobalt2_e : 0.000012

Product: (mmol/gDw/h)
  EX_h2o_e : 48.004573
  EX_co2_e : 29.066022
  EX_h_e : 7.365322
  EX_succ_e : 0.500715
  Auxiliary production reaction : 0.253559
  EX_ura_e : 0.086950
  DM_5drib_c : 0.000108
  DM_4crsol_c : 0.000107
  EX_etha_e : 0.000039

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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