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 : 2p4c2me_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (69 of 116: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 25
  Gene deletion: b2744 b3614 b0910 b4152 b2781 b1612 b1611 b4122 b1759 b4374 b0675 b4388 b4138 b4123 b0621 b4381 b2406 b3453 b2197 b2835 b3918 b1912 b2240 b1206 b3924   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.697570 (mmol/gDw/h)
  Minimum Production Rate : 0.156042 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 991.291090
  EX_o2_e : 273.634091
  EX_glc__D_e : 10.000000
  EX_nh4_e : 8.679096
  EX_pi_e : 1.353382
  EX_so4_e : 0.175662
  EX_k_e : 0.136161
  EX_mg2_e : 0.006051
  EX_ca2_e : 0.003631
  EX_cl_e : 0.003631
  EX_cu2_e : 0.000495
  EX_mn2_e : 0.000482
  EX_zn2_e : 0.000238
  EX_ni2_e : 0.000225
  EX_cobalt2_e : 0.000017

Product: (mmol/gDw/h)
  EX_fe3_e : 999.988796
  EX_h2o_e : 546.678336
  EX_co2_e : 24.282020
  EX_succ_e : 0.727420
  EX_ura_e : 0.338638
  EX_glyc3p_e : 0.212376
  Auxiliary production reaction : 0.156042
  DM_5drib_c : 0.000157
  DM_4crsol_c : 0.000156

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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