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 : 2h3oppan_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (62 of 85: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 29
  Gene deletion: b3553 b1478 b1241 b0351 b4069 b3115 b1849 b2296 b3617 b1004 b3713 b1109 b0046 b3236 b1033 b1602 b2913 b4381 b0114 b0509 b3125 b0755 b3612 b0529 b2492 b0904 b1380 b1517 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.406923 (mmol/gDw/h)
  Minimum Production Rate : 0.197092 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 993.271496
  EX_o2_e : 287.813474
  EX_glc__D_e : 10.000000
  EX_nh4_e : 4.781228
  EX_pi_e : 0.392521
  EX_so4_e : 0.102471
  EX_k_e : 0.079429
  EX_mg2_e : 0.003530
  EX_ca2_e : 0.002118
  EX_cl_e : 0.002118
  EX_cu2_e : 0.000289
  EX_mn2_e : 0.000281
  EX_zn2_e : 0.000139
  EX_ni2_e : 0.000131
  EX_cobalt2_e : 0.000010

Product: (mmol/gDw/h)
  EX_fe3_e : 999.993464
  EX_h2o_e : 549.619184
  EX_co2_e : 37.906660
  EX_ac_e : 2.012920
  DM_oxam_c : 0.386492
  Auxiliary production reaction : 0.197092
  DM_mththf_c : 0.000182
  DM_5drib_c : 0.000092
  DM_4crsol_c : 0.000091

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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