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 (53 of 77: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 38
  Gene deletion: b3553 b1478 b4382 b1241 b4069 b4384 b2297 b2458 b2779 b2407 b1004 b3713 b1109 b0046 b3236 b2210 b1033 b0411 b2799 b3945 b1602 b3915 b3654 b3714 b3664 b4064 b4464 b0529 b2492 b0904 b1380 b2660 b1695 b1518 b0606 b2285 b1007 b4209   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.383027 (mmol/gDw/h)
  Minimum Production Rate : 1.048322 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 995.203128
  EX_o2_e : 284.626154
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.233303
  EX_pi_e : 2.466114
  EX_so4_e : 0.096454
  EX_k_e : 0.074764
  EX_mg2_e : 0.003323
  EX_ca2_e : 0.001994
  EX_cl_e : 0.001994
  EX_cu2_e : 0.000272
  EX_mn2_e : 0.000265
  EX_zn2_e : 0.000131
  EX_ni2_e : 0.000124

Product: (mmol/gDw/h)
  EX_fe3_e : 999.993848
  EX_h2o_e : 552.894942
  EX_co2_e : 34.396758
  Auxiliary production reaction : 1.048322
  EX_ac_e : 0.222993
  DM_mththf_c : 0.000172
  DM_5drib_c : 0.000086
  DM_4crsol_c : 0.000085

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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