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 : paps_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (34 of 36: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 40
  Gene deletion: b4467 b4382 b4069 b4384 b3708 b3115 b1849 b2296 b2926 b0030 b2407 b1004 b3713 b1109 b0046 b3236 b1982 b2797 b3117 b1814 b4471 b0261 b0411 b1602 b2913 b2406 b3915 b0452 b1727 b0114 b1539 b2492 b0904 b1533 b1380 b1771 b0606 b2285 b1008 b4209   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.463551 (mmol/gDw/h)
  Minimum Production Rate : 0.196360 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 36.447791
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.990179
  EX_pi_e : 0.839861
  EX_so4_e : 0.313091
  EX_k_e : 0.090482
  EX_fe3_e : 0.007447
  EX_mg2_e : 0.004021
  EX_ca2_e : 0.002413
  EX_cl_e : 0.002413
  EX_cu2_e : 0.000329
  EX_mn2_e : 0.000320
  EX_zn2_e : 0.000158
  EX_ni2_e : 0.000150
  EX_cobalt2_e : 0.000012

Product: (mmol/gDw/h)
  EX_h2o_e : 51.937856
  EX_co2_e : 37.326695
  EX_h_e : 5.127762
  EX_12ppd__R_e : 0.379903
  EX_ac_e : 0.269874
  Auxiliary production reaction : 0.196359
  EX_hxan_e : 0.000519
  DM_5drib_c : 0.000311
  DM_4crsol_c : 0.000103

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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