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 : nadhx__R_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (74 of 116: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 33
  Gene deletion: b3553 b3399 b4382 b1241 b0351 b4069 b2744 b3708 b2297 b2458 b3617 b0160 b1982 b2797 b3117 b1814 b4471 b1033 b0675 b2361 b0261 b4381 b2406 b0112 b0114 b0509 b3125 b2366 b2492 b0904 b1533 b3825 b0494   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.499001 (mmol/gDw/h)
  Minimum Production Rate : 0.733544 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 21.082608
  EX_nh4_e : 10.537595
  EX_glc__D_e : 10.000000
  EX_pi_e : 1.948428
  EX_so4_e : 0.125659
  EX_k_e : 0.097402
  EX_fe2_e : 0.008014
  EX_mg2_e : 0.004329
  EX_ca2_e : 0.002597
  EX_cl_e : 0.002597
  EX_cu2_e : 0.000354
  EX_mn2_e : 0.000345
  EX_zn2_e : 0.000170
  EX_ni2_e : 0.000161
  EX_cobalt2_e : 0.000012

Product: (mmol/gDw/h)
  EX_h2o_e : 47.434959
  EX_co2_e : 20.293148
  EX_h_e : 10.176160
  EX_ac_e : 1.895853
  Auxiliary production reaction : 0.733544
  DM_oxam_c : 0.013615
  DM_5drib_c : 0.000335
  EX_glyclt_e : 0.000334
  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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