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 : 12ppd__S_e
List of minimal gene deletion strategies (Download)

Gene deletion strategy (66 of 92: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 33
  Gene deletion: b3553 b4382 b3942 b1732 b1241 b0351 b4384 b0871 b2407 b1004 b3713 b1109 b0046 b3236 b1779 b2210 b1033 b3945 b1602 b2913 b3915 b1727 b0529 b2492 b0904 b3821 b1380 b1517 b0606 b0221 b2285 b1011 b4209   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.497241 (mmol/gDw/h)
  Minimum Production Rate : 0.131370 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 38.000859
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.370160
  EX_pi_e : 0.479642
  EX_so4_e : 0.125216
  EX_k_e : 0.097058
  EX_fe3_e : 0.007988
  EX_mg2_e : 0.004314
  EX_ca2_e : 0.002588
  EX_cl_e : 0.002588
  EX_cu2_e : 0.000353
  EX_mn2_e : 0.000344
  EX_zn2_e : 0.000170
  EX_ni2_e : 0.000161
  EX_cobalt2_e : 0.000012

Product: (mmol/gDw/h)
  EX_h2o_e : 52.190746
  EX_co2_e : 39.195342
  EX_h_e : 4.576837
  EX_12ppd__S_e : 0.131362
  EX_mththf_e : 0.000223
  DM_5drib_c : 0.000112
  DM_4crsol_c : 0.000111

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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