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 : uacgam_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (63 of 74: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 33
  Gene deletion: b1241 b0351 b2744 b3614 b0910 b4152 b2925 b2097 b2781 b3124 b1612 b1611 b4122 b0907 b2690 b1759 b4374 b0675 b3945 b4138 b4123 b0621 b4381 b2406 b3453 b0755 b3612 b2197 b2835 b3918 b1912 b2240 b1206   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.598454 (mmol/gDw/h)
  Minimum Production Rate : 0.316070 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 992.196988
  EX_o2_e : 275.775134
  EX_glc__D_e : 10.000000
  EX_nh4_e : 7.628105
  EX_pi_e : 1.209413
  EX_so4_e : 0.150703
  EX_k_e : 0.116814
  EX_mg2_e : 0.005192
  EX_cl_e : 0.003115
  EX_ca2_e : 0.003115
  EX_cu2_e : 0.000424
  EX_mn2_e : 0.000414
  EX_zn2_e : 0.000204
  EX_ni2_e : 0.000193
  EX_cobalt2_e : 0.000015

Product: (mmol/gDw/h)
  EX_fe3_e : 999.990388
  EX_h2o_e : 546.547180
  EX_co2_e : 26.106029
  EX_succ_e : 0.624063
  EX_ac_e : 0.513728
  Auxiliary production reaction : 0.316070
  EX_ura_e : 0.108322
  DM_5drib_c : 0.000135
  DM_4crsol_c : 0.000133

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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