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 (70 of 75: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 35
  Gene deletion: b2836 b0474 b2518 b2744 b4152 b2297 b2458 b2925 b2097 b2781 b1238 b1612 b1611 b4122 b1779 b1759 b3946 b0825 b2440 b4374 b4161 b0675 b4138 b4123 b0621 b4381 b2406 b0529 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 : 0.359208 (mmol/gDw/h)
  Minimum Production Rate : 0.189685 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 991.600205
  EX_o2_e : 281.651297
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.337335
  EX_pi_e : 0.725864
  EX_so4_e : 0.090456
  EX_k_e : 0.070115
  EX_mg2_e : 0.003116
  EX_ca2_e : 0.001870
  EX_cl_e : 0.001870
  EX_cu2_e : 0.000255
  EX_mn2_e : 0.000248
  EX_zn2_e : 0.000122
  EX_ni2_e : 0.000116

Product: (mmol/gDw/h)
  EX_fe3_e : 999.994231
  EX_h2o_e : 546.590416
  EX_co2_e : 31.085756
  EX_succ_e : 1.713232
  EX_ac_e : 0.209126
  Auxiliary production reaction : 0.189685
  EX_ura_e : 0.065047
  DM_5drib_c : 0.000081
  DM_4crsol_c : 0.000080
  EX_etha_e : 0.000029

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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