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 : 2ombzl_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (69 of 85: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 31
  Gene deletion: b3399 b2502 b4384 b2744 b3708 b3008 b0871 b2925 b2097 b1779 b2690 b2797 b3117 b1814 b4471 b2440 b3665 b0675 b2361 b3945 b4381 b2406 b3654 b3714 b3664 b0114 b1539 b2492 b0904 b1533 b3927   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.642451 (mmol/gDw/h)
  Minimum Production Rate : 0.039412 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 26.431836
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.955221
  EX_pi_e : 0.619712
  EX_so4_e : 0.161782
  EX_k_e : 0.125402
  EX_fe2_e : 0.010318
  EX_mg2_e : 0.005573
  EX_ca2_e : 0.003344
  EX_cl_e : 0.003344
  EX_cu2_e : 0.000455
  EX_mn2_e : 0.000444
  EX_zn2_e : 0.000219
  EX_ni2_e : 0.000208
  EX_cobalt2_e : 0.000016

Product: (mmol/gDw/h)
  EX_h2o_e : 46.523707
  EX_co2_e : 27.764633
  EX_h_e : 7.263291
  EX_pyr_e : 1.326578
  Auxiliary production reaction : 0.039412
  DM_oxam_c : 0.016810
  DM_5drib_c : 0.000145
  DM_4crsol_c : 0.000143

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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