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 (68 of 82: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 40
  Gene deletion: b4467 b2836 b4384 b2744 b3708 b3008 b0871 b2926 b2407 b1004 b3713 b1109 b0046 b2688 b2797 b3117 b1814 b4471 b2210 b0411 b1602 b4381 b3654 b2868 b3714 b3664 b4064 b4464 b0114 b2366 b0529 b2492 b0904 b2578 b1533 b3927 b1380 b3662 b1517 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.483601 (mmol/gDw/h)
  Minimum Production Rate : 0.111642 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 38.335986
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.780931
  EX_pi_e : 0.912949
  EX_so4_e : 0.121781
  EX_k_e : 0.094396
  EX_fe2_e : 0.007769
  EX_mg2_e : 0.004195
  EX_ca2_e : 0.002517
  EX_cl_e : 0.002517
  EX_cu2_e : 0.000343
  EX_mn2_e : 0.000334
  EX_zn2_e : 0.000165
  EX_ni2_e : 0.000156
  EX_cobalt2_e : 0.000012

Product: (mmol/gDw/h)
  EX_h2o_e : 53.477963
  EX_co2_e : 39.033153
  EX_h_e : 4.778368
  Auxiliary production reaction : 0.111616
  EX_mththf_e : 0.000217
  DM_5drib_c : 0.000109
  DM_4crsol_c : 0.000108

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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