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 : 2dr1p_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (40 of 40: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 39
  Gene deletion: b4467 b1478 b3399 b1241 b4069 b4384 b2744 b2297 b2458 b2779 b2926 b3844 b1004 b3713 b1109 b0046 b3236 b1638 b3908 b1656 b0937 b4139 b3665 b0675 b2361 b4015 b3945 b1602 b4381 b0529 b1539 b2492 b0904 b2954 b1380 b2660 b1517 b2285 b1008   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.475862 (mmol/gDw/h)
  Minimum Production Rate : 0.212457 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 995.341309
  EX_o2_e : 287.726192
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.140867
  EX_pi_e : 0.671476
  EX_so4_e : 0.119831
  EX_k_e : 0.092885
  EX_mg2_e : 0.004128
  EX_ca2_e : 0.002477
  EX_cl_e : 0.002477
  EX_cu2_e : 0.000337
  EX_mn2_e : 0.000329
  EX_zn2_e : 0.000162
  EX_ni2_e : 0.000154
  EX_cobalt2_e : 0.000012

Product: (mmol/gDw/h)
  EX_fe3_e : 999.992357
  EX_h2o_e : 551.627060
  EX_co2_e : 38.849029
  EX_ac_e : 0.277040
  Auxiliary production reaction : 0.212457
  EX_ade_e : 0.000320
  EX_mththf_e : 0.000213
  DM_5drib_c : 0.000107
  DM_4crsol_c : 0.000106

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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