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 : unagamuf_p
List of minimal gene deletion strategies (Download)

Gene deletion strategy (74 of 79: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 41
  Gene deletion: b0945 b2836 b3399 b4382 b0238 b0125 b1241 b0351 b4069 b4384 b2744 b3708 b2297 b2458 b3617 b2407 b3236 b4139 b2797 b3117 b1814 b4471 b0675 b2361 b0112 b3654 b2868 b3714 b3664 b4064 b4464 b0114 b1539 b2492 b0904 b2954 b1533 b0723 b1511 b3662 b1985   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.530453 (mmol/gDw/h)
  Minimum Production Rate : 0.104154 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 991.826204
  EX_o2_e : 268.657658
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.796779
  EX_pi_e : 0.719987
  EX_so4_e : 0.133579
  EX_k_e : 0.103541
  EX_mg2_e : 0.004602
  EX_cl_e : 0.002761
  EX_ca2_e : 0.002761
  EX_cu2_e : 0.000376
  EX_mn2_e : 0.000367
  EX_zn2_e : 0.000181
  EX_ni2_e : 0.000171
  EX_cobalt2_e : 0.000013

Product: (mmol/gDw/h)
  EX_fe3_e : 999.991480
  EX_h2o_e : 540.680145
  EX_co2_e : 21.565659
  EX_ac_e : 1.221181
  EX_succ_e : 0.553152
  EX_thymd_e : 0.377733
  Auxiliary production reaction : 0.104154
  DM_mththf_c : 0.000238
  DM_5drib_c : 0.000119
  DM_4crsol_c : 0.000118

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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