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 : 4r5au_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (93 of 111: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 34
  Gene deletion: b3399 b2502 b2744 b3708 b3008 b0871 b0583 b0121 b1982 b2797 b3117 b1814 b4471 b4374 b0675 b2361 b0261 b4381 b2406 b3453 b0452 b0114 b0886 b1539 b2492 b0904 b2578 b1533 b3927 b3825 b3029 b2240 b4141 b1798   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.766807 (mmol/gDw/h)
  Minimum Production Rate : 0.004238 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 25.037958
  EX_glc__D_e : 10.000000
  EX_nh4_e : 9.204950
  EX_pi_e : 0.741696
  EX_so4_e : 0.193097
  EX_k_e : 0.149675
  EX_fe2_e : 0.012316
  EX_mg2_e : 0.006652
  EX_ca2_e : 0.003991
  EX_cl_e : 0.003991
  EX_cu2_e : 0.000544
  EX_mn2_e : 0.000530
  EX_zn2_e : 0.000261
  EX_ni2_e : 0.000248
  EX_cobalt2_e : 0.000019

Product: (mmol/gDw/h)
  EX_h2o_e : 48.759067
  EX_co2_e : 26.213780
  EX_h_e : 7.969228
  EX_thym_e : 0.453271
  Auxiliary production reaction : 0.004238
  EX_glyc3p_e : 0.002029
  DM_5drib_c : 0.000515
  DM_4crsol_c : 0.000171

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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