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 (63 of 82: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 36
  Gene deletion: b1478 b4269 b3942 b1732 b0493 b3588 b3003 b3011 b1241 b0351 b4384 b1278 b1479 b0871 b2925 b2097 b0030 b2407 b3236 b0517 b2690 b2463 b1982 b3616 b3589 b2210 b0675 b0822 b4381 b2406 b0114 b0529 b2492 b0904 b3662 b1517   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.583027 (mmol/gDw/h)
  Minimum Production Rate : 0.622428 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 25.186192
  EX_glc__D_e : 10.000000
  EX_nh4_e : 9.408778
  EX_pi_e : 3.052102
  EX_so4_e : 0.146818
  EX_k_e : 0.113803
  EX_fe2_e : 0.009364
  EX_mg2_e : 0.005058
  EX_ca2_e : 0.003035
  EX_cl_e : 0.003035
  EX_cu2_e : 0.000413
  EX_mn2_e : 0.000403
  EX_zn2_e : 0.000199
  EX_ni2_e : 0.000188
  EX_cobalt2_e : 0.000015

Product: (mmol/gDw/h)
  EX_h2o_e : 50.026290
  EX_co2_e : 25.293750
  EX_h_e : 7.224366
  EX_acald_e : 1.461040
  Auxiliary production reaction : 0.622428
  DM_mththf_c : 0.325604
  DM_5drib_c : 0.000391
  DM_4crsol_c : 0.000130

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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