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_p
List of minimal gene deletion strategies (Download)

Gene deletion strategy (29 of 41: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 32
  Gene deletion: b4467 b2242 b0474 b2518 b3831 b2781 b0030 b1004 b3713 b1109 b0046 b1612 b1611 b4122 b0651 b2162 b1759 b2210 b4161 b1415 b0411 b4138 b4123 b0621 b4381 b3028 b3918 b4042 b1206 b2285 b3893 b1474   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.576999 (mmol/gDw/h)
  Minimum Production Rate : 0.304739 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 992.665889
  EX_o2_e : 280.429950
  EX_glc__D_e : 10.000000
  EX_nh4_e : 7.049892
  EX_pi_e : 0.556576
  EX_so4_e : 0.145300
  EX_k_e : 0.112626
  EX_mg2_e : 0.005005
  EX_ca2_e : 0.003003
  EX_cl_e : 0.003003
  EX_cu2_e : 0.000409
  EX_mn2_e : 0.000399
  EX_zn2_e : 0.000197
  EX_ni2_e : 0.000186
  EX_cobalt2_e : 0.000014

Product: (mmol/gDw/h)
  EX_fe3_e : 999.990733
  EX_h2o_e : 548.932898
  EX_co2_e : 30.748275
  EX_succ_e : 0.601690
  Auxiliary production reaction : 0.304739
  EX_ura_e : 0.104438
  EX_for_e : 0.001415
  DM_5drib_c : 0.000130
  DM_4crsol_c : 0.000129

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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