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 : 4r5au_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (37 of 111: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 26
  Gene deletion: b3553 b3399 b1241 b0351 b4069 b2502 b2744 b2297 b2458 b2926 b1982 b3616 b3589 b1033 b0675 b2361 b2291 b0261 b4381 b0112 b0114 b0509 b3125 b0529 b2492 b0904   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.452652 (mmol/gDw/h)
  Minimum Production Rate : 0.668097 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 25.114164
  EX_glc__D_e : 10.000000
  EX_nh4_e : 9.695285
  EX_pi_e : 0.436631
  EX_so4_e : 0.113987
  EX_k_e : 0.088354
  EX_fe2_e : 0.007270
  EX_mg2_e : 0.003927
  EX_ca2_e : 0.002356
  EX_cl_e : 0.002356
  EX_cu2_e : 0.000321
  EX_mn2_e : 0.000313
  EX_zn2_e : 0.000154
  EX_ni2_e : 0.000146
  EX_cobalt2_e : 0.000011

Product: (mmol/gDw/h)
  EX_h2o_e : 47.242171
  EX_co2_e : 24.209832
  EX_h_e : 9.229863
  EX_thymd_e : 1.066893
  Auxiliary production reaction : 0.668097
  EX_ac_e : 0.263528
  DM_oxam_c : 0.000507
  DM_5drib_c : 0.000304
  DM_4crsol_c : 0.000101

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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