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 (29 of 83: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 33
  Gene deletion: b3553 b1478 b4382 b0238 b0125 b1241 b4069 b4384 b2297 b2458 b1004 b3713 b1109 b0046 b3236 b1779 b0477 b1033 b2799 b3945 b1602 b3915 b0452 b0529 b2492 b0904 b1380 b2660 b1518 b0606 b2285 b1011 b4209   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.446549 (mmol/gDw/h)
  Minimum Production Rate : 0.678882 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 994.573876
  EX_o2_e : 285.122839
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.878599
  EX_pi_e : 1.109626
  EX_so4_e : 0.112450
  EX_k_e : 0.087163
  EX_mg2_e : 0.003874
  EX_ca2_e : 0.002324
  EX_cl_e : 0.002324
  EX_cu2_e : 0.000317
  EX_mn2_e : 0.000309
  EX_zn2_e : 0.000152
  EX_ni2_e : 0.000144
  EX_cobalt2_e : 0.000011

Product: (mmol/gDw/h)
  EX_fe3_e : 999.992828
  EX_h2o_e : 549.921409
  EX_co2_e : 35.757079
  Auxiliary production reaction : 0.678882
  EX_hxan_e : 0.263976
  EX_ac_e : 0.259975
  DM_mththf_c : 0.000200
  DM_5drib_c : 0.000100
  DM_4crsol_c : 0.000100

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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