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 : dhpt_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (69 of 115: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 29
  Gene deletion: b3553 b3399 b1241 b0351 b4069 b2502 b2744 b0512 b2297 b2458 b2779 b2926 b0907 b1982 b3616 b3589 b1033 b4374 b0675 b2361 b2291 b0261 b0112 b2789 b3127 b0114 b0529 b2492 b0904   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.319737 (mmol/gDw/h)
  Minimum Production Rate : 1.225536 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 25.871785
  EX_nh4_e : 10.807784
  EX_glc__D_e : 10.000000
  EX_pi_e : 0.308421
  EX_so4_e : 0.080516
  EX_k_e : 0.062410
  EX_fe2_e : 0.005135
  EX_mg2_e : 0.002774
  EX_ca2_e : 0.001664
  EX_cl_e : 0.001664
  EX_cu2_e : 0.000227
  EX_mn2_e : 0.000221
  EX_zn2_e : 0.000109
  EX_ni2_e : 0.000103

Product: (mmol/gDw/h)
  EX_h2o_e : 50.930891
  EX_co2_e : 22.876429
  EX_h_e : 14.938145
  EX_ac_e : 2.194407
  EX_glyclt_e : 1.225679
  Auxiliary production reaction : 1.225536
  EX_alltn_e : 0.000358
  DM_5drib_c : 0.000215
  DM_4crsol_c : 0.000071

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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