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 : prbatp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (44 of 47: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 42
  Gene deletion: b3399 b0474 b2518 b1241 b0351 b2744 b3708 b3008 b2930 b4232 b3697 b3925 b0512 b0871 b2779 b2926 b3617 b0160 b1982 b2797 b3117 b1814 b4471 b3946 b0825 b4374 b0675 b2361 b2291 b0261 b0452 b0114 b2366 b0529 b2492 b0904 b2578 b1533 b3927 b3825 b3447 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.350017 (mmol/gDw/h)
  Minimum Production Rate : 0.079338 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 991.057403
  EX_o2_e : 280.183963
  EX_glc__D_e : 10.000000
  EX_nh4_e : 4.182312
  EX_pi_e : 0.654982
  EX_so4_e : 0.088141
  EX_k_e : 0.068321
  EX_mg2_e : 0.003036
  EX_ca2_e : 0.001822
  EX_cl_e : 0.001822
  EX_cu2_e : 0.000248
  EX_mn2_e : 0.000242
  EX_zn2_e : 0.000119
  EX_ni2_e : 0.000113

Product: (mmol/gDw/h)
  EX_fe3_e : 999.994378
  EX_h2o_e : 543.992181
  EX_co2_e : 27.993196
  EX_pyr_e : 5.476910
  Auxiliary production reaction : 0.079338
  EX_alltn_e : 0.001366
  DM_5drib_c : 0.001210
  DM_4crsol_c : 0.001053
  EX_glyc__R_e : 0.000487

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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