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 : dudp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (63 of 77: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 42
  Gene deletion: b2836 b3399 b4382 b4069 b2744 b3708 b3008 b2297 b2458 b2883 b2797 b3117 b1814 b4471 b1623 b3665 b3709 b4381 b2406 b3161 b0112 b3654 b3714 b3664 b4064 b4464 b0114 b1539 b2492 b0904 b2578 b1533 b3927 b1473 b0594 b3447 b4141 b1798 b3662 b1517 b0221 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.526242 (mmol/gDw/h)
  Minimum Production Rate : 0.629438 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 31.620859
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.956015
  EX_pi_e : 1.766492
  EX_so4_e : 0.132518
  EX_k_e : 0.102719
  EX_fe2_e : 0.008452
  EX_mg2_e : 0.004565
  EX_ca2_e : 0.002739
  EX_cl_e : 0.002739
  EX_cu2_e : 0.000373
  EX_mn2_e : 0.000364
  EX_zn2_e : 0.000179
  EX_ni2_e : 0.000170
  EX_cobalt2_e : 0.000013

Product: (mmol/gDw/h)
  EX_h2o_e : 51.053419
  EX_co2_e : 32.093779
  EX_h_e : 5.798671
  Auxiliary production reaction : 0.629438
  EX_ac_e : 0.306371
  DM_oxam_c : 0.013770
  DM_mththf_c : 0.000236
  DM_5drib_c : 0.000118
  DM_4crsol_c : 0.000117

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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