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 : lald__D_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (40 of 80: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 29
  Gene deletion: b4467 b1478 b4269 b0493 b3588 b3003 b3011 b1241 b4384 b0871 b2926 b2407 b3844 b1004 b3713 b1109 b0046 b3236 b1602 b0153 b2492 b0904 b3035 b1380 b2660 b1771 b0606 b2285 b1007   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.510205 (mmol/gDw/h)
  Minimum Production Rate : 0.098213 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 995.303841
  EX_o2_e : 286.904531
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.510167
  EX_pi_e : 0.492146
  EX_so4_e : 0.128480
  EX_k_e : 0.099588
  EX_mg2_e : 0.004426
  EX_ca2_e : 0.002656
  EX_cl_e : 0.002656
  EX_cu2_e : 0.000362
  EX_mn2_e : 0.000353
  EX_zn2_e : 0.000174
  EX_ni2_e : 0.000165
  EX_cobalt2_e : 0.000013

Product: (mmol/gDw/h)
  EX_fe3_e : 999.991806
  EX_h2o_e : 551.616232
  EX_co2_e : 38.147235
  Auxiliary production reaction : 0.303736
  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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