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 : thmnp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (50 of 87: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 30
  Gene deletion: b3553 b3399 b4382 b1241 b0351 b4069 b4384 b2744 b3115 b1849 b2296 b3617 b0160 b3124 b1982 b1033 b0675 b2361 b2291 b0261 b0112 b2789 b3127 b0114 b0755 b3612 b0529 b2492 b0904 b0514   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.477012 (mmol/gDw/h)
  Minimum Production Rate : 0.704052 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 23.236756
  EX_nh4_e : 10.921096
  EX_glc__D_e : 10.000000
  EX_pi_e : 0.460128
  EX_so4_e : 0.120121
  EX_k_e : 0.093109
  EX_fe2_e : 0.007661
  EX_mg2_e : 0.004138
  EX_cl_e : 0.002483
  EX_ca2_e : 0.002483
  EX_cu2_e : 0.000338
  EX_mn2_e : 0.000330
  EX_zn2_e : 0.000163
  EX_ni2_e : 0.000154
  EX_cobalt2_e : 0.000012

Product: (mmol/gDw/h)
  EX_h2o_e : 47.963703
  EX_co2_e : 22.283757
  EX_h_e : 10.430627
  EX_thymd_e : 1.124309
  Auxiliary production reaction : 0.704052
  EX_ac_e : 0.277710
  DM_oxam_c : 0.000534
  DM_5drib_c : 0.000320
  DM_4crsol_c : 0.000106

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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