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 : aconm_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (97 of 99: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 46
  Gene deletion: b4467 b2836 b1478 b4269 b0493 b3588 b3003 b3011 b1241 b4384 b3752 b0871 b2779 b2407 b1004 b3713 b1109 b0046 b3236 b1638 b1982 b0477 b4139 b0261 b2799 b3945 b1602 b4381 b2406 b3915 b2975 b3603 b0509 b3125 b0529 b2492 b0904 b1300 b2954 b3029 b1380 b0508 b2660 b3662 b2285 b1011   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.461497 (mmol/gDw/h)
  Minimum Production Rate : 0.191725 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 38.438864
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.945342
  EX_pi_e : 0.445163
  EX_so4_e : 0.116214
  EX_k_e : 0.090081
  EX_fe3_e : 0.007412
  EX_mg2_e : 0.004003
  EX_ca2_e : 0.002402
  EX_cl_e : 0.002402
  EX_cu2_e : 0.000327
  EX_mn2_e : 0.000319
  EX_zn2_e : 0.000157
  EX_ni2_e : 0.000149
  EX_cobalt2_e : 0.000012

Product: (mmol/gDw/h)
  EX_h2o_e : 53.434093
  EX_co2_e : 38.753335
  EX_h_e : 5.592494
  EX_ade_e : 0.192242
  Auxiliary production reaction : 0.191725
  DM_5drib_c : 0.000310
  DM_4crsol_c : 0.000103

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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