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 : ppgpp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (81 of 82: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 53
  Gene deletion: b4467 b3399 b0474 b2518 b4069 b2744 b2930 b4232 b3697 b3925 b0871 b3115 b1849 b2296 b2779 b0160 b1238 b1004 b3713 b1109 b0046 b3236 b1638 b0477 b4139 b3946 b0825 b0675 b2361 b0411 b2799 b3945 b1602 b2913 b4381 b3915 b0452 b3654 b2868 b3714 b3664 b1727 b4064 b4464 b0114 b0529 b2492 b0904 b3029 b1380 b1511 b2285 b1009   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.324731 (mmol/gDw/h)
  Minimum Production Rate : 0.150273 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 30.554900
  EX_glc__D_e : 10.000000
  EX_nh4_e : 4.258429
  EX_pi_e : 0.914328
  EX_so4_e : 0.081774
  EX_k_e : 0.063385
  EX_fe3_e : 0.005216
  EX_mg2_e : 0.002817
  EX_ca2_e : 0.001690
  EX_cl_e : 0.001690
  EX_cu2_e : 0.000230
  EX_mn2_e : 0.000224
  EX_zn2_e : 0.000111
  EX_ni2_e : 0.000105

Product: (mmol/gDw/h)
  EX_h2o_e : 44.423366
  EX_co2_e : 28.000095
  EX_h_e : 9.225389
  EX_pyr_e : 5.596545
  EX_ac_e : 0.189054
  Auxiliary production reaction : 0.150273
  DM_mththf_c : 0.000145
  DM_5drib_c : 0.000073
  DM_4crsol_c : 0.000072

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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