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 : uacmamu_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (60 of 74: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 34
  Gene deletion: b0474 b2518 b3831 b1278 b3752 b4152 b2297 b2458 b2925 b2097 b2781 b1612 b1611 b4122 b1779 b2690 b1759 b4161 b4015 b0411 b1701 b1805 b3945 b4138 b4123 b0621 b2913 b4381 b0529 b2197 b3918 b1206 b2285 b1378   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.379009 (mmol/gDw/h)
  Minimum Production Rate : 0.200172 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 991.191296
  EX_o2_e : 281.191534
  EX_glc__D_e : 10.000000
  EX_nh4_e : 4.830985
  EX_pi_e : 0.765938
  EX_so4_e : 0.095442
  EX_k_e : 0.073980
  EX_mg2_e : 0.003288
  EX_ca2_e : 0.001973
  EX_cl_e : 0.001973
  EX_cu2_e : 0.000269
  EX_mn2_e : 0.000262
  EX_zn2_e : 0.000129
  EX_ni2_e : 0.000122

Product: (mmol/gDw/h)
  EX_fe3_e : 999.993913
  EX_h2o_e : 544.346761
  EX_co2_e : 31.200923
  EX_ac_e : 3.992127
  EX_succ_e : 0.395228
  Auxiliary production reaction : 0.200172
  EX_ura_e : 0.068602
  DM_5drib_c : 0.000085
  DM_4crsol_c : 0.000085

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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