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 : ahdt_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (53 of 83: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 30
  Gene deletion: b3553 b3399 b4382 b1241 b0351 b4069 b2502 b4384 b2744 b2297 b2458 b2779 b2407 b1982 b3616 b3589 b1033 b0675 b2361 b0261 b0112 b2789 b3127 b0114 b0755 b3612 b0529 b2492 b0904 b0514   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.479536 (mmol/gDw/h)
  Minimum Production Rate : 0.707777 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 23.396116
  EX_nh4_e : 10.978883
  EX_glc__D_e : 10.000000
  EX_pi_e : 2.585894
  EX_so4_e : 0.120757
  EX_k_e : 0.093602
  EX_fe2_e : 0.007702
  EX_mg2_e : 0.004160
  EX_ca2_e : 0.002496
  EX_cl_e : 0.002496
  EX_cu2_e : 0.000340
  EX_mn2_e : 0.000331
  EX_zn2_e : 0.000164
  EX_ni2_e : 0.000155
  EX_cobalt2_e : 0.000012

Product: (mmol/gDw/h)
  EX_h2o_e : 50.731122
  EX_co2_e : 22.084185
  EX_h_e : 9.070265
  EX_thymd_e : 1.130258
  Auxiliary production reaction : 0.707777
  EX_ac_e : 0.279179
  DM_oxam_c : 0.000537
  DM_5drib_c : 0.000322
  DM_4crsol_c : 0.000107

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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