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 : pgp160_p
List of minimal gene deletion strategies (Download)

Gene deletion strategy (91 of 98: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 35
  Gene deletion: b0474 b2518 b3831 b1278 b3752 b4152 b2925 b2097 b2781 b3236 b1612 b1611 b4122 b1638 b1779 b2690 b1759 b3449 b4161 b3945 b4138 b4123 b0621 b2913 b4381 b2239 b2406 b0452 b0529 b2197 b3029 b3918 b0418 b1206 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.386559 (mmol/gDw/h)
  Minimum Production Rate : 0.204128 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 28.771642
  EX_glc__D_e : 10.000000
  EX_nh4_e : 4.723094
  EX_pi_e : 0.781165
  EX_so4_e : 0.097343
  EX_k_e : 0.075454
  EX_fe2_e : 0.003707
  EX_mg2_e : 0.003353
  EX_fe3_e : 0.002501
  EX_ca2_e : 0.002012
  EX_cl_e : 0.002012
  EX_cu2_e : 0.000274
  EX_mn2_e : 0.000267
  EX_zn2_e : 0.000132
  EX_ni2_e : 0.000125

Product: (mmol/gDw/h)
  EX_h2o_e : 44.639272
  EX_co2_e : 32.046405
  EX_h_e : 5.515245
  EX_ac_e : 0.810585
  EX_succ_e : 0.403101
  EX_ura_e : 0.274128
  Auxiliary production reaction : 0.204128
  DM_5drib_c : 0.000087
  DM_4crsol_c : 0.000086
  EX_g3pe_e : 0.000031

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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