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 : seramp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (70 of 80: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 36
  Gene deletion: b3553 b4069 b4384 b3708 b3926 b2297 b2458 b0030 b2407 b1004 b3713 b1109 b0046 b3236 b1638 b1982 b4139 b2797 b3117 b1814 b4471 b1033 b1602 b4381 b0114 b1539 b2492 b0904 b1533 b3825 b3029 b1380 b0494 b2660 b1518 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.504956 (mmol/gDw/h)
  Minimum Production Rate : 0.128519 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 36.322030
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.224592
  EX_pi_e : 0.615602
  EX_so4_e : 0.127158
  EX_k_e : 0.098564
  EX_fe2_e : 0.008110
  EX_mg2_e : 0.004380
  EX_ca2_e : 0.002628
  EX_cl_e : 0.002628
  EX_cu2_e : 0.000358
  EX_mn2_e : 0.000349
  EX_zn2_e : 0.000172
  EX_ni2_e : 0.000163
  EX_cobalt2_e : 0.000013

Product: (mmol/gDw/h)
  EX_h2o_e : 52.147806
  EX_co2_e : 37.014058
  EX_h_e : 5.447788
  EX_ac_e : 0.293978
  Auxiliary production reaction : 0.128519
  DM_mththf_c : 0.000226
  DM_5drib_c : 0.000114
  DM_4crsol_c : 0.000113

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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