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 : fprica_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (76 of 80: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 39
  Gene deletion: b3500 b3399 b4382 b0474 b2518 b2502 b4384 b2744 b3708 b3008 b0871 b2781 b0099 b0030 b2235 b2883 b0517 b1982 b2797 b3117 b1814 b4471 b1623 b0507 b4064 b4464 b0114 b0886 b0529 b1539 b2492 b0904 b2954 b1533 b3927 b3821 b2413 b1511 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.577648 (mmol/gDw/h)
  Minimum Production Rate : 0.131068 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 994.149769
  EX_o2_e : 284.059150
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.771843
  EX_pi_e : 0.688271
  EX_so4_e : 0.145463
  EX_k_e : 0.112753
  EX_mg2_e : 0.005011
  EX_ca2_e : 0.003007
  EX_cl_e : 0.003007
  EX_cu2_e : 0.000410
  EX_mn2_e : 0.000399
  EX_zn2_e : 0.000197
  EX_ni2_e : 0.000187
  EX_cobalt2_e : 0.000014

Product: (mmol/gDw/h)
  EX_fe3_e : 999.990722
  EX_h2o_e : 551.535790
  EX_co2_e : 34.959875
  Auxiliary production reaction : 0.131068
  EX_alltn_e : 0.002255
  DM_mththf_c : 0.001868
  DM_5drib_c : 0.000388
  DM_4crsol_c : 0.000129

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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