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 : sbt6p_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (11 of 83: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 30
  Gene deletion: b3553 b1478 b1241 b4069 b3115 b1849 b2296 b2926 b1004 b3713 b1109 b0046 b3236 b1033 b2799 b3945 b1602 b2913 b4381 b3915 b0529 b2492 b0904 b1380 b1511 b0606 b0221 b2285 b1010 b4209   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.425895 (mmol/gDw/h)
  Minimum Production Rate : 0.944538 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 995.043571
  EX_o2_e : 284.479337
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.387975
  EX_pi_e : 1.355358
  EX_so4_e : 0.107249
  EX_k_e : 0.083132
  EX_mg2_e : 0.003695
  EX_cl_e : 0.002217
  EX_ca2_e : 0.002217
  EX_cu2_e : 0.000302
  EX_mn2_e : 0.000294
  EX_zn2_e : 0.000145
  EX_ni2_e : 0.000138
  EX_cobalt2_e : 0.000011

Product: (mmol/gDw/h)
  EX_fe3_e : 999.993160
  EX_h2o_e : 548.386531
  EX_co2_e : 35.369465
  Auxiliary production reaction : 0.944538
  EX_ac_e : 0.247950
  EX_hxan_e : 0.197087
  DM_mththf_c : 0.000191
  DM_5drib_c : 0.000096
  DM_4crsol_c : 0.000095

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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