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 : pnto__R_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (39 of 79: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 34
  Gene deletion: b4382 b1241 b0351 b4384 b3708 b3008 b3752 b0871 b2297 b2458 b2925 b2097 b2407 b2797 b3117 b1814 b4471 b3616 b3589 b3946 b0825 b3665 b2406 b3654 b3714 b3664 b0114 b2366 b2492 b0904 b1533 b3927 b3821 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.511712 (mmol/gDw/h)
  Minimum Production Rate : 0.354086 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 992.018776
  EX_o2_e : 277.954106
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.880533
  EX_pi_e : 0.493601
  EX_so4_e : 0.128859
  EX_k_e : 0.099883
  EX_mg2_e : 0.004439
  EX_ca2_e : 0.002663
  EX_cl_e : 0.002663
  EX_cu2_e : 0.000363
  EX_mn2_e : 0.000354
  EX_zn2_e : 0.000174
  EX_ni2_e : 0.000165
  EX_cobalt2_e : 0.000013

Product: (mmol/gDw/h)
  EX_fe3_e : 999.991781
  EX_h2o_e : 544.900724
  EX_co2_e : 28.120741
  EX_pyr_e : 2.563018
  Auxiliary production reaction : 0.354086
  DM_5drib_c : 0.000115
  DM_4crsol_c : 0.000114

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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