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

Gene deletion strategy (66 of 74: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 28
  Gene deletion: b3942 b1732 b2066 b0474 b2518 b1241 b0351 b2744 b0871 b3115 b1849 b2296 b2925 b2097 b2781 b0099 b0160 b3236 b2690 b3616 b3589 b2361 b2291 b3945 b2943 b0114 b2492 b0904   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.758208 (mmol/gDw/h)
  Minimum Production Rate : 0.555342 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 26.145894
  EX_glc__D_e : 10.000000
  EX_nh4_e : 8.748363
  EX_pi_e : 0.731372
  EX_so4_e : 0.190932
  EX_k_e : 0.147997
  EX_fe2_e : 0.012178
  EX_mg2_e : 0.006577
  EX_ca2_e : 0.003946
  EX_cl_e : 0.003946
  EX_cu2_e : 0.000538
  EX_mn2_e : 0.000524
  EX_zn2_e : 0.000259
  EX_ni2_e : 0.000245
  EX_cobalt2_e : 0.000019

Product: (mmol/gDw/h)
  EX_h2o_e : 48.344401
  EX_co2_e : 27.202662
  EX_h_e : 7.529459
  Auxiliary production reaction : 0.556822
  DM_oxam_c : 0.002960
  DM_5drib_c : 0.000171
  DM_4crsol_c : 0.000169

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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