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 (109 of 116: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 44
  Gene deletion: b3553 b3399 b4269 b0493 b3588 b3003 b3011 b4384 b2744 b0871 b2925 b2097 b2926 b0160 b2407 b1004 b3713 b1109 b0046 b3236 b1638 b2690 b1982 b4139 b1033 b0675 b2361 b0261 b2799 b3945 b1602 b2342 b3845 b4381 b1727 b0114 b0529 b2492 b0904 b3927 b3029 b1380 b2660 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.345990 (mmol/gDw/h)
  Minimum Production Rate : 0.092528 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 30.086247
  EX_glc__D_e : 10.000000
  EX_nh4_e : 4.384361
  EX_pi_e : 0.518801
  EX_so4_e : 0.087127
  EX_k_e : 0.067535
  EX_fe3_e : 0.045513
  EX_mg2_e : 0.003001
  EX_ca2_e : 0.001801
  EX_cl_e : 0.001801
  EX_cu2_e : 0.000245
  EX_mn2_e : 0.000239
  EX_zn2_e : 0.000118
  EX_ni2_e : 0.000112

Product: (mmol/gDw/h)
  EX_h2o_e : 44.126673
  EX_co2_e : 27.954711
  EX_h_e : 8.987290
  EX_pyr_e : 5.300040
  Auxiliary production reaction : 0.092528
  EX_fe2_e : 0.039956
  DM_5drib_c : 0.000232
  DM_4crsol_c : 0.000077

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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