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 (61 of 82: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 35
  Gene deletion: b3942 b1732 b0474 b2518 b4069 b4384 b2744 b3708 b3008 b0512 b3115 b1849 b2296 b2926 b0030 b2407 b3236 b1982 b2797 b3117 b1814 b4471 b2210 b0411 b4381 b0511 b0114 b2366 b2492 b0904 b1533 b3927 b3821 b3662 b1517   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.658345 (mmol/gDw/h)
  Minimum Production Rate : 0.279265 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 28.849246
  EX_glc__D_e : 10.000000
  EX_nh4_e : 8.508173
  EX_pi_e : 1.752105
  EX_so4_e : 0.165785
  EX_k_e : 0.128504
  EX_fe2_e : 0.010574
  EX_mg2_e : 0.005711
  EX_ca2_e : 0.003427
  EX_cl_e : 0.003427
  EX_cu2_e : 0.000467
  EX_mn2_e : 0.000455
  EX_zn2_e : 0.000224
  EX_ni2_e : 0.000213
  EX_cobalt2_e : 0.000016

Product: (mmol/gDw/h)
  EX_h2o_e : 50.993092
  EX_co2_e : 29.415044
  EX_h_e : 7.271988
  EX_ac_e : 0.383279
  Auxiliary production reaction : 0.279265
  EX_xan_e : 0.000443
  DM_mththf_c : 0.000295
  DM_5drib_c : 0.000148
  DM_4crsol_c : 0.000147

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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