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 : ap4a_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (69 of 70: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 47
  Gene deletion: b3500 b4467 b1478 b4382 b0474 b2518 b1241 b0351 b4384 b3752 b0871 b2925 b2097 b2926 b2781 b0099 b0160 b2235 b3844 b1004 b3713 b1109 b0046 b3236 b2690 b1982 b1623 b4015 b0261 b0411 b2799 b3945 b1602 b2913 b3915 b4064 b4464 b0529 b2492 b0904 b2954 b3927 b1380 b0515 b0606 b2285 b1010   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.375259 (mmol/gDw/h)
  Minimum Production Rate : 0.006683 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 30.467072
  EX_glc__D_e : 10.000000
  EX_nh4_e : 4.121695
  EX_pi_e : 0.388710
  EX_so4_e : 0.094498
  EX_k_e : 0.073248
  EX_fe3_e : 0.006027
  EX_mg2_e : 0.003255
  EX_cl_e : 0.001953
  EX_ca2_e : 0.001953
  EX_cu2_e : 0.000266
  EX_mn2_e : 0.000259
  EX_zn2_e : 0.000128
  EX_ni2_e : 0.000121

Product: (mmol/gDw/h)
  EX_h2o_e : 43.971335
  EX_co2_e : 28.589859
  EX_h_e : 8.786550
  EX_pyr_e : 5.290296
  Auxiliary production reaction : 0.006683
  EX_ade_e : 0.000420
  DM_5drib_c : 0.000252
  DM_4crsol_c : 0.000084

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.

Last updated: 21-Sep-2023
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