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 : uaccg_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (61 of 75: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 26
  Gene deletion: b4382 b0474 b2518 b3831 b4384 b3752 b4152 b2781 b1612 b1611 b4122 b2388 b1759 b0394 b4161 b4388 b4138 b4123 b0621 b2406 b0452 b2197 b3825 b3918 b1912 b1206   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.657118 (mmol/gDw/h)
  Minimum Production Rate : 0.194379 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 25.049843
  EX_glc__D_e : 10.000000
  EX_nh4_e : 8.223181
  EX_pi_e : 1.022618
  EX_so4_e : 0.165475
  EX_k_e : 0.128265
  EX_fe2_e : 0.010554
  EX_mg2_e : 0.005700
  EX_ca2_e : 0.003420
  EX_cl_e : 0.003420
  EX_cu2_e : 0.000466
  EX_mn2_e : 0.000454
  EX_zn2_e : 0.000224
  EX_ni2_e : 0.000212
  EX_cobalt2_e : 0.000016

Product: (mmol/gDw/h)
  EX_h2o_e : 47.236247
  EX_co2_e : 25.313347
  EX_h_e : 8.340320
  EX_succ_e : 0.685237
  EX_ura_e : 0.271614
  Auxiliary production reaction : 0.194379
  DM_5drib_c : 0.000148
  DM_4crsol_c : 0.000147

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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