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 : 4fe4s_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (13 of 16: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 26
  Gene deletion: b3399 b2744 b3708 b3008 b0871 b3236 b1779 b2797 b3117 b1814 b4471 b1623 b3665 b0675 b2361 b4381 b3453 b0114 b1539 b2492 b0904 b1533 b3825 b2240 b0516 b1517   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.709786 (mmol/gDw/h)
  Minimum Production Rate : 0.054468 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 993.283573
  EX_o2_e : 278.865833
  EX_glc__D_e : 10.000000
  EX_nh4_e : 7.739923
  EX_pi_e : 0.684664
  EX_so4_e : 0.396612
  EX_k_e : 0.138545
  EX_mg2_e : 0.006157
  EX_ca2_e : 0.003694
  EX_cl_e : 0.003694
  EX_cu2_e : 0.000503
  EX_mn2_e : 0.000490
  EX_zn2_e : 0.000242
  EX_ni2_e : 0.000229
  EX_cobalt2_e : 0.000018

Product: (mmol/gDw/h)
  EX_fe3_e : 999.770727
  EX_h2o_e : 549.603983
  EX_co2_e : 30.790647
  Auxiliary production reaction : 0.054468
  EX_alltn_e : 0.018572
  DM_mththf_c : 0.000318
  DM_5drib_c : 0.000160
  DM_4crsol_c : 0.000158

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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