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 : utp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (62 of 78: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 28
  Gene deletion: b0474 b2518 b3831 b3752 b2930 b4232 b3697 b3925 b4152 b2926 b2781 b1232 b1612 b1611 b4122 b2690 b1759 b4161 b0411 b3945 b4138 b4123 b0621 b4381 b3918 b4042 b1206 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.498643 (mmol/gDw/h)
  Minimum Production Rate : 0.263356 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 30.919221
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.092531
  EX_pi_e : 1.271063
  EX_so4_e : 0.125568
  EX_k_e : 0.097332
  EX_fe2_e : 0.008009
  EX_mg2_e : 0.004326
  EX_ca2_e : 0.002595
  EX_cl_e : 0.002595
  EX_cu2_e : 0.000354
  EX_mn2_e : 0.000345
  EX_zn2_e : 0.000170
  EX_ni2_e : 0.000161
  EX_cobalt2_e : 0.000012

Product: (mmol/gDw/h)
  EX_h2o_e : 47.702188
  EX_co2_e : 31.192927
  EX_h_e : 7.566658
  EX_ac_e : 1.764448
  EX_succ_e : 0.519981
  Auxiliary production reaction : 0.263356
  EX_ura_e : 0.090256
  DM_5drib_c : 0.000112
  DM_4crsol_c : 0.000111

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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