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 : ddca_p
List of minimal gene deletion strategies (Download)

Gene deletion strategy (57 of 76: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 25
  Gene deletion: b4382 b0474 b2518 b3831 b4384 b1278 b3752 b4152 b2781 b1612 b1611 b4122 b2029 b1759 b4161 b4138 b4123 b0621 b2406 b0452 b0529 b2197 b3918 b1206 b4209   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.473776 (mmol/gDw/h)
  Minimum Production Rate : 0.249755 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 982.770941
  EX_o2_e : 260.808980
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.788693
  EX_pi_e : 0.457007
  EX_so4_e : 0.119306
  EX_k_e : 0.092478
  EX_mg2_e : 0.004110
  EX_cl_e : 0.002466
  EX_ca2_e : 0.002466
  EX_cu2_e : 0.000336
  EX_mn2_e : 0.000327
  EX_zn2_e : 0.000162
  EX_ni2_e : 0.000153
  EX_cobalt2_e : 0.000012

Product: (mmol/gDw/h)
  EX_fe3_e : 999.992391
  EX_h2o_e : 527.000953
  EX_co2_e : 12.319714
  EX_ac_e : 10.958400
  EX_succ_e : 0.494050
  EX_ura_e : 0.335977
  Auxiliary production reaction : 0.249755
  DM_5drib_c : 0.000107
  DM_4crsol_c : 0.000106

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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