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 : dutp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (79 of 79: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 52
  Gene deletion: b3399 b4069 b2502 b2744 b3708 b3008 b2297 b2458 b3236 b3962 b0593 b2688 b2797 b3117 b1814 b4471 b4267 b2265 b1623 b3665 b4374 b0675 b2361 b2291 b0411 b0822 b3709 b3161 b0112 b2943 b3654 b3714 b3664 b0837 b0124 b0114 b0529 b1539 b2492 b0904 b2578 b1533 b3927 b3821 b0325 b2413 b0508 b1473 b1511 b4266 b4141 b1798   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.510931 (mmol/gDw/h)
  Minimum Production Rate : 0.651231 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 32.132410
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.820468
  EX_pi_e : 2.446538
  EX_so4_e : 0.128663
  EX_k_e : 0.099730
  EX_fe2_e : 0.008206
  EX_mg2_e : 0.004432
  EX_ca2_e : 0.002659
  EX_cl_e : 0.002659
  EX_cu2_e : 0.000362
  EX_mn2_e : 0.000353
  EX_zn2_e : 0.000174
  EX_ni2_e : 0.000165
  EX_cobalt2_e : 0.000013

Product: (mmol/gDw/h)
  EX_h2o_e : 51.924854
  EX_co2_e : 32.571515
  EX_h_e : 4.992090
  Auxiliary production reaction : 0.651231
  EX_ac_e : 0.297457
  DM_mththf_c : 0.000229
  DM_5drib_c : 0.000115
  DM_4crsol_c : 0.000114

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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