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 : prbatp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (33 of 47: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 35
  Gene deletion: b2836 b3553 b4382 b4069 b4384 b3708 b3008 b3752 b2297 b2458 b2925 b2097 b2407 b2690 b1982 b2797 b3117 b1814 b4471 b1033 b0596 b0261 b3945 b2406 b0114 b0509 b3125 b2366 b2492 b0904 b2947 b2578 b1533 b3927 b3662   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.720479 (mmol/gDw/h)
  Minimum Production Rate : 0.303316 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 24.257588
  EX_glc__D_e : 10.000000
  EX_nh4_e : 9.298502
  EX_pi_e : 1.908243
  EX_so4_e : 0.181431
  EX_k_e : 0.140633
  EX_fe2_e : 0.011572
  EX_mg2_e : 0.006250
  EX_ca2_e : 0.003750
  EX_cl_e : 0.003750
  EX_cu2_e : 0.000511
  EX_mn2_e : 0.000498
  EX_zn2_e : 0.000246
  EX_ni2_e : 0.000233
  EX_cobalt2_e : 0.000018

Product: (mmol/gDw/h)
  EX_h2o_e : 48.916305
  EX_co2_e : 25.035767
  EX_h_e : 7.951065
  EX_ac_e : 0.419453
  Auxiliary production reaction : 0.303316
  DM_oxam_c : 0.000806
  DM_5drib_c : 0.000483
  DM_4crsol_c : 0.000161

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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