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 : dcyt_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (34 of 41: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 43
  Gene deletion: b3399 b4382 b4069 b4384 b2744 b3708 b3008 b3115 b1849 b2296 b0160 b2407 b0583 b1982 b2797 b3117 b1814 b4471 b3665 b0675 b2361 b0261 b0507 b2342 b3845 b3709 b2406 b3161 b0112 b0452 b2975 b0114 b3603 b0886 b2366 b2492 b0904 b2578 b1533 b3927 b1473 b4141 b1798   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.679276 (mmol/gDw/h)
  Minimum Production Rate : 0.863219 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 22.968988
  EX_glc__D_e : 10.000000
  EX_nh4_e : 9.929584
  EX_pi_e : 0.655234
  EX_so4_e : 0.171055
  EX_k_e : 0.132590
  EX_fe2_e : 0.010910
  EX_mg2_e : 0.005893
  EX_ca2_e : 0.003536
  EX_cl_e : 0.003536
  EX_cu2_e : 0.000482
  EX_mn2_e : 0.000469
  EX_zn2_e : 0.000232
  EX_ni2_e : 0.000219
  EX_cobalt2_e : 0.000017

Product: (mmol/gDw/h)
  EX_h2o_e : 47.541554
  EX_co2_e : 23.553610
  EX_h_e : 9.230385
  Auxiliary production reaction : 0.863219
  EX_ac_e : 0.395465
  EX_ade_e : 0.000760
  DM_5drib_c : 0.000456
  DM_4crsol_c : 0.000151

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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