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 : nadhx__R_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (72 of 116: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 32
  Gene deletion: b3553 b1478 b3846 b2341 b1241 b0351 b3708 b2779 b3844 b1004 b3713 b1109 b0046 b3236 b1779 b2920 b3619 b1033 b2799 b3945 b1602 b2913 b2789 b3127 b3915 b0728 b0529 b1380 b3546 b0606 b2285 b1009   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.591142 (mmol/gDw/h)
  Minimum Production Rate : 0.021750 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 994.450106
  EX_o2_e : 284.070074
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.536535
  EX_pi_e : 0.613720
  EX_so4_e : 0.148861
  EX_k_e : 0.115387
  EX_mg2_e : 0.005128
  EX_ca2_e : 0.003077
  EX_cl_e : 0.003077
  EX_cu2_e : 0.000419
  EX_mn2_e : 0.000408
  EX_zn2_e : 0.000202
  EX_ni2_e : 0.000191
  EX_cobalt2_e : 0.000015

Product: (mmol/gDw/h)
  EX_fe3_e : 999.990506
  EX_h2o_e : 551.298514
  EX_co2_e : 35.279582
  Auxiliary production reaction : 0.021750
  DM_5drib_c : 0.000133
  DM_4crsol_c : 0.000132

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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