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 (79 of 79: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 76
  Gene deletion: b4467 b2836 b2242 b4269 b0493 b3588 b3003 b3011 b0474 b2518 b1241 b0351 b3831 b2744 b1278 b3708 b3008 b0871 b2926 b2781 b0030 b3844 b1612 b1611 b2883 b4122 b0651 b2162 b1759 b3962 b1525 b0104 b2797 b3117 b1814 b4471 b3616 b3589 b4267 b4161 b0675 b1415 b1014 b0411 b0822 b2799 b1907 b4138 b4123 b0621 b4381 b2406 b0112 b3915 b2868 b0114 b0509 b3125 b0755 b3612 b0529 b1539 b2492 b0904 b1533 b3028 b1380 b3918 b1473 b0594 b0514 b1511 b4266 b3662 b2842 b1206   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.350141 (mmol/gDw/h)
  Minimum Production Rate : 0.090431 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 35.169979
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.364968
  EX_pi_e : 0.426637
  EX_so4_e : 0.088173
  EX_k_e : 0.068345
  EX_fe3_e : 0.005625
  EX_mg2_e : 0.003037
  EX_ca2_e : 0.001822
  EX_cl_e : 0.001822
  EX_cu2_e : 0.000248
  EX_mn2_e : 0.000242
  EX_zn2_e : 0.000119
  EX_ni2_e : 0.000113

Product: (mmol/gDw/h)
  EX_h2o_e : 51.017840
  EX_co2_e : 34.683917
  EX_h_e : 7.587091
  EX_acald_e : 1.529758
  EX_succ_e : 0.934706
  EX_hxan_e : 0.569582
  Auxiliary production reaction : 0.088890
  EX_thym_e : 0.063686
  EX_dxylnt_e : 0.000234
  DM_mththf_c : 0.000157
  DM_5drib_c : 0.000079
  DM_4crsol_c : 0.000078

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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