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 : dnad_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (59 of 84: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 39
  Gene deletion: b3399 b0586 b2502 b4384 b2744 b3708 b3008 b0871 b1779 b0120 b1982 b2797 b3117 b1814 b4471 b2440 b3665 b4374 b0675 b2361 b2291 b0261 b0507 b3709 b3161 b0112 b0452 b0114 b0886 b1539 b2492 b0904 b2578 b1533 b3927 b1473 b4141 b1798 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.485659 (mmol/gDw/h)
  Minimum Production Rate : 0.111657 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 37.020798
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.916525
  EX_pi_e : 0.691368
  EX_so4_e : 0.122300
  EX_k_e : 0.094797
  EX_fe2_e : 0.007802
  EX_mg2_e : 0.004213
  EX_ca2_e : 0.002528
  EX_cl_e : 0.002528
  EX_cu2_e : 0.000344
  EX_mn2_e : 0.000336
  EX_zn2_e : 0.000166
  EX_ni2_e : 0.000157
  EX_cobalt2_e : 0.000012

Product: (mmol/gDw/h)
  EX_h2o_e : 52.780950
  EX_co2_e : 37.721628
  EX_h_e : 4.910940
  Auxiliary production reaction : 0.111449
  EX_ade_e : 0.000543
  DM_5drib_c : 0.000326
  DM_4crsol_c : 0.000108
  EX_etha_e : 0.000039

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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