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 : uacmam_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: b3831 b3614 b0910 b3752 b4152 b2781 b1612 b1611 b4122 b1759 b2440 b4388 b4138 b4123 b0621 b4381 b2239 b2406 b2197 b3918 b1912 b1206 b2285 b3893 b1474   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.524954 (mmol/gDw/h)
  Minimum Production Rate : 0.277252 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 30.881883
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.691249
  EX_pi_e : 1.060877
  EX_so4_e : 0.132194
  EX_k_e : 0.102467
  EX_fe2_e : 0.008431
  EX_mg2_e : 0.004554
  EX_ca2_e : 0.002732
  EX_cl_e : 0.002732
  EX_cu2_e : 0.000372
  EX_mn2_e : 0.000363
  EX_zn2_e : 0.000179
  EX_ni2_e : 0.000170
  EX_cobalt2_e : 0.000013

Product: (mmol/gDw/h)
  EX_h2o_e : 49.104890
  EX_co2_e : 31.170032
  EX_h_e : 6.385609
  EX_succ_e : 0.547418
  Auxiliary production reaction : 0.277252
  EX_ura_e : 0.095018
  DM_5drib_c : 0.000118
  DM_4crsol_c : 0.000117

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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