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 (72 of 79: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 34
  Gene deletion: b2242 b3553 b0474 b2518 b2744 b2779 b2781 b1004 b3713 b1109 b0046 b1612 b1611 b4122 b1759 b2210 b1033 b4374 b4161 b0675 b1415 b4388 b4138 b4123 b0621 b4381 b3028 b3918 b1912 b1206 b2285 b3893 b1474 b3924   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.457031 (mmol/gDw/h)
  Minimum Production Rate : 0.118643 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 36.838190
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.584104
  EX_pi_e : 0.559498
  EX_so4_e : 0.115090
  EX_k_e : 0.089209
  EX_fe2_e : 0.007340
  EX_mg2_e : 0.003965
  EX_ca2_e : 0.002379
  EX_cl_e : 0.002379
  EX_cu2_e : 0.000324
  EX_mn2_e : 0.000316
  EX_zn2_e : 0.000156
  EX_ni2_e : 0.000148
  EX_cobalt2_e : 0.000011

Product: (mmol/gDw/h)
  EX_h2o_e : 51.729663
  EX_co2_e : 37.207699
  EX_h_e : 5.682125
  EX_succ_e : 0.476589
  EX_ura_e : 0.205460
  Auxiliary production reaction : 0.118643
  DM_5drib_c : 0.000103
  DM_4crsol_c : 0.000102

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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