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 : uri_e
List of minimal gene deletion strategies (Download)

Gene deletion strategy (53 of 77: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 29
  Gene deletion: b0474 b2518 b3831 b3752 b3926 b2930 b4232 b3697 b3925 b4152 b2297 b2458 b2926 b2781 b3236 b1612 b1611 b4122 b0907 b2690 b1759 b4161 b3945 b4138 b4123 b0621 b1380 b3918 b1206   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.588372 (mmol/gDw/h)
  Minimum Production Rate : 0.310746 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 991.227740
  EX_o2_e : 277.495865
  EX_glc__D_e : 10.000000
  EX_nh4_e : 7.188859
  EX_pi_e : 0.567548
  EX_so4_e : 0.148164
  EX_k_e : 0.114846
  EX_mg2_e : 0.005104
  EX_ca2_e : 0.003062
  EX_cl_e : 0.003062
  EX_cu2_e : 0.000417
  EX_mn2_e : 0.000407
  EX_zn2_e : 0.000201
  EX_ni2_e : 0.000190
  EX_cobalt2_e : 0.000015

Product: (mmol/gDw/h)
  EX_fe3_e : 999.990550
  EX_h2o_e : 546.602383
  EX_co2_e : 27.583066
  EX_succ_e : 1.089790
  EX_ac_e : 0.342542
  EX_uri_e : 0.310746
  EX_ura_e : 0.106497
  DM_5drib_c : 0.000132
  DM_4crsol_c : 0.000131

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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