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 : nmn_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (62 of 79: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 26
  Gene deletion: b3831 b3614 b0910 b4152 b2779 b2781 b0030 b1612 b1611 b4122 b0651 b2162 b1759 b0411 b4138 b4123 b0621 b2913 b4381 b0529 b2835 b3918 b4042 b0494 b1206 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.515245 (mmol/gDw/h)
  Minimum Production Rate : 0.272124 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 993.724212
  EX_o2_e : 282.778953
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.295375
  EX_pi_e : 0.769133
  EX_so4_e : 0.129749
  EX_k_e : 0.100572
  EX_mg2_e : 0.004470
  EX_ca2_e : 0.002682
  EX_cl_e : 0.002682
  EX_cu2_e : 0.000365
  EX_mn2_e : 0.000356
  EX_zn2_e : 0.000176
  EX_ni2_e : 0.000166
  EX_cobalt2_e : 0.000013

Product: (mmol/gDw/h)
  EX_fe3_e : 999.991725
  EX_h2o_e : 550.118622
  EX_co2_e : 33.335966
  EX_succ_e : 0.537294
  Auxiliary production reaction : 0.272124
  EX_ura_e : 0.093261
  DM_5drib_c : 0.000116
  DM_4crsol_c : 0.000115

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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