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 : udpglcur_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (66 of 75: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 30
  Gene deletion: b2836 b1241 b0351 b3831 b4069 b3614 b0910 b3752 b4152 b2297 b2458 b2781 b1612 b1611 b4122 b1779 b1759 b3616 b3589 b0411 b4388 b4138 b4123 b0621 b4381 b0529 b3918 b4042 b1206 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.480101 (mmol/gDw/h)
  Minimum Production Rate : 0.253524 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 992.698081
  EX_o2_e : 281.220625
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.865971
  EX_pi_e : 0.970156
  EX_so4_e : 0.120899
  EX_k_e : 0.093712
  EX_mg2_e : 0.004165
  EX_cl_e : 0.002499
  EX_ca2_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_fe3_e : 999.992289
  EX_h2o_e : 547.377410
  EX_co2_e : 31.232557
  EX_ac_e : 1.454161
  EX_succ_e : 0.500645
  Auxiliary production reaction : 0.253524
  EX_ura_e : 0.086938
  DM_5drib_c : 0.000108
  DM_4crsol_c : 0.000107

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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