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 : gsn_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (62 of 79: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 32
  Gene deletion: b4269 b0493 b3588 b3003 b3011 b2066 b0474 b2518 b1241 b0351 b4384 b3752 b0871 b3617 b2407 b0517 b1982 b2498 b2406 b2943 b0114 b0509 b3125 b0529 b2492 b0904 b3437 b4268 b0508 b3662 b1518 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.445551 (mmol/gDw/h)
  Minimum Production Rate : 0.350872 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 33.456491
  EX_glc__D_e : 10.000000
  EX_nh4_e : 8.061933
  EX_pi_e : 0.429781
  EX_so4_e : 0.112199
  EX_k_e : 0.086968
  EX_fe2_e : 0.007156
  EX_mg2_e : 0.003865
  EX_ca2_e : 0.002319
  EX_cl_e : 0.002319
  EX_cu2_e : 0.000316
  EX_mn2_e : 0.000308
  EX_zn2_e : 0.000152
  EX_ni2_e : 0.000144
  EX_cobalt2_e : 0.000011

Product: (mmol/gDw/h)
  EX_h2o_e : 52.336542
  EX_co2_e : 32.977246
  EX_h_e : 7.344219
  EX_acald_e : 0.744354
  EX_thym_e : 0.744354
  Auxiliary production reaction : 0.350872
  EX_alltn_e : 0.001739
  DM_mththf_c : 0.001440
  DM_5drib_c : 0.000299
  EX_glyclt_e : 0.000298
  DM_4crsol_c : 0.000099

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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