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 : gtp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (70 of 70: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 56
  Gene deletion: b3553 b3399 b4382 b2066 b4069 b4384 b2744 b3708 b0910 b3115 b1849 b2296 b2925 b2097 b0160 b0030 b1004 b3713 b1109 b0046 b3236 b2883 b1638 b1779 b2690 b1982 b4139 b2797 b3117 b1814 b4471 b2498 b1033 b2361 b2291 b0261 b1602 b2913 b2406 b2868 b1727 b4064 b4464 b0114 b2366 b2492 b0904 b1533 b3927 b3825 b3029 b1380 b1771 b3662 b2285 b1007   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.410413 (mmol/gDw/h)
  Minimum Production Rate : 0.173850 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 38.720221
  EX_glc__D_e : 10.000000
  EX_fe3_e : 6.702705
  EX_nh4_e : 5.452546
  EX_pi_e : 0.917437
  EX_so4_e : 0.103350
  EX_k_e : 0.080110
  EX_mg2_e : 0.003560
  EX_ca2_e : 0.002136
  EX_cl_e : 0.002136
  EX_cu2_e : 0.000291
  EX_mn2_e : 0.000284
  EX_zn2_e : 0.000140
  EX_ni2_e : 0.000133
  EX_cobalt2_e : 0.000010

Product: (mmol/gDw/h)
  EX_h2o_e : 50.934141
  EX_co2_e : 40.637692
  EX_h_e : 11.385101
  EX_fe2_e : 6.696113
  EX_ac_e : 0.238937
  Auxiliary production reaction : 0.173850
  EX_ura_e : 0.074286
  EX_ade_e : 0.000459
  DM_5drib_c : 0.000275
  DM_4crsol_c : 0.000092

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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