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 : urdgci_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (75 of 75: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 55
  Gene deletion: b2836 b3553 b1478 b3399 b4269 b0493 b3588 b3003 b3011 b0238 b0125 b1241 b0351 b4384 b2744 b0871 b2926 b3617 b2407 b1004 b3713 b1109 b0046 b3236 b1638 b2937 b3908 b1656 b4139 b1033 b0675 b2361 b2799 b3945 b1602 b0507 b2913 b4381 b3915 b3654 b3714 b3664 b0511 b4064 b4464 b2492 b0904 b2954 b1380 b2965 b0693 b0515 b1518 b2285 b1011   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.491570 (mmol/gDw/h)
  Minimum Production Rate : 0.016289 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 36.669833
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.357694
  EX_pi_e : 0.474171
  EX_so4_e : 0.123788
  EX_k_e : 0.095951
  EX_fe3_e : 0.007897
  EX_mg2_e : 0.004264
  EX_ca2_e : 0.002559
  EX_cl_e : 0.002559
  EX_cu2_e : 0.000349
  EX_mn2_e : 0.000340
  EX_zn2_e : 0.000168
  EX_ni2_e : 0.000159
  EX_cobalt2_e : 0.000012

Product: (mmol/gDw/h)
  EX_h2o_e : 51.147428
  EX_co2_e : 38.105333
  EX_h_e : 4.573419
  EX_acald_e : 0.834050
  Auxiliary production reaction : 0.016261
  DM_mththf_c : 0.000220
  DM_5drib_c : 0.000111
  DM_4crsol_c : 0.000110

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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