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 : dctp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (58 of 73: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 42
  Gene deletion: b4382 b3942 b1732 b1241 b0351 b4069 b4384 b3708 b1479 b3752 b2297 b2458 b3617 b2407 b3844 b3236 b2463 b1982 b2797 b3117 b1814 b4471 b2210 b3665 b3551 b4219 b1832 b1778 b2406 b0452 b0114 b2366 b2492 b0904 b1533 b1710 b2480 b1511 b3662 b1206 b0606 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.412221 (mmol/gDw/h)
  Minimum Production Rate : 1.234008 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 29.141763
  EX_glc__D_e : 10.000000
  EX_nh4_e : 8.155362
  EX_pi_e : 4.099654
  EX_so4_e : 0.103805
  EX_k_e : 0.080463
  EX_fe2_e : 0.006621
  EX_mg2_e : 0.003576
  EX_ca2_e : 0.002146
  EX_cl_e : 0.002146
  EX_cu2_e : 0.000292
  EX_mn2_e : 0.000285
  EX_zn2_e : 0.000141
  EX_ni2_e : 0.000133
  EX_cobalt2_e : 0.000010

Product: (mmol/gDw/h)
  EX_h2o_e : 52.444023
  EX_co2_e : 28.357944
  EX_h_e : 6.829995
  Auxiliary production reaction : 1.234008
  EX_ac_e : 0.949337
  EX_fum_e : 0.428806
  EX_ade_e : 0.000277
  EX_mththf_e : 0.000185
  DM_5drib_c : 0.000093
  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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