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 (76 of 77: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 53
  Gene deletion: b4467 b2836 b2242 b1241 b0351 b3831 b3708 b3614 b0910 b0871 b2926 b2781 b0030 b3844 b1004 b3713 b1109 b0046 b3236 b1612 b1611 b4122 b0651 b2162 b1759 b0937 b2797 b3117 b1814 b4471 b0261 b2799 b3945 b1602 b4138 b4123 b0621 b4381 b1727 b2366 b0529 b2492 b0904 b3927 b3028 b1380 b3918 b4042 b2660 b1206 b0606 b2285 b1011   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.452404 (mmol/gDw/h)
  Minimum Production Rate : 0.021720 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 994.372110
  EX_o2_e : 287.271223
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.406153
  EX_pi_e : 0.436392
  EX_so4_e : 0.113924
  EX_k_e : 0.088306
  EX_mg2_e : 0.003925
  EX_ca2_e : 0.002355
  EX_cl_e : 0.002355
  EX_cu2_e : 0.000321
  EX_mn2_e : 0.000313
  EX_zn2_e : 0.000154
  EX_ni2_e : 0.000146
  EX_cobalt2_e : 0.000011

Product: (mmol/gDw/h)
  EX_fe3_e : 999.992734
  EX_h2o_e : 551.506059
  EX_co2_e : 37.612429
  EX_succ_e : 0.471764
  EX_uri_e : 0.178189
  EX_ura_e : 0.081923
  DM_5drib_c : 0.000102
  DM_4crsol_c : 0.000101

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.

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Last updated: 21-Sep-2023
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