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 (40 of 82: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 27
  Gene deletion: b3399 b1241 b0351 b4069 b2502 b2744 b2297 b2458 b3236 b0907 b1779 b1982 b3616 b3589 b2210 b1623 b3665 b0675 b2361 b4381 b0112 b0114 b0529 b2492 b0904 b0516 b1517   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.487033 (mmol/gDw/h)
  Minimum Production Rate : 0.920968 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 27.690146
  EX_glc__D_e : 10.000000
  EX_nh4_e : 9.917371
  EX_pi_e : 4.153669
  EX_so4_e : 0.122645
  EX_k_e : 0.095065
  EX_fe2_e : 0.007822
  EX_mg2_e : 0.004225
  EX_ca2_e : 0.002535
  EX_cl_e : 0.002535
  EX_cu2_e : 0.000345
  EX_mn2_e : 0.000337
  EX_zn2_e : 0.000166
  EX_ni2_e : 0.000157
  EX_cobalt2_e : 0.000012

Product: (mmol/gDw/h)
  EX_h2o_e : 52.695735
  EX_co2_e : 25.927529
  EX_h_e : 9.699880
  EX_ac_e : 2.409307
  Auxiliary production reaction : 0.920968
  EX_alltn_e : 0.012744
  EX_ade_e : 0.000328
  DM_mththf_c : 0.000218
  DM_5drib_c : 0.000110
  DM_4crsol_c : 0.000109

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.

Last updated: 21-Sep-2023
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