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 : aacoa_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (54 of 84: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 53
  Gene deletion: b3553 b1478 b1241 b0351 b4069 b4384 b3708 b3752 b2297 b2458 b1238 b1004 b3713 b1109 b0046 b3236 b1779 b0121 b1982 b2797 b3117 b1814 b4471 b1033 b0261 b0411 b2799 b3945 b1602 b0507 b3709 b2913 b4381 b2406 b3161 b0112 b3915 b0452 b4064 b4464 b1539 b2492 b0904 b1533 b1380 b4042 b1473 b4141 b1798 b0606 b2285 b1010 b4209   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.376573 (mmol/gDw/h)
  Minimum Production Rate : 0.128454 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 35.894006
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.965014
  EX_pi_e : 0.748597
  EX_so4_e : 0.223280
  EX_k_e : 0.073504
  EX_fe3_e : 0.006050
  EX_mg2_e : 0.003267
  EX_cl_e : 0.001960
  EX_ca2_e : 0.001960
  EX_cu2_e : 0.000267
  EX_mn2_e : 0.000260
  EX_zn2_e : 0.000128
  EX_ni2_e : 0.000122

Product: (mmol/gDw/h)
  EX_h2o_e : 52.464714
  EX_co2_e : 35.329018
  EX_h_e : 7.602499
  EX_ac_e : 1.752092
  EX_xan_e : 0.499199
  Auxiliary production reaction : 0.128451
  EX_ade_e : 0.000421
  DM_5drib_c : 0.000253
  DM_4crsol_c : 0.000084

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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