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 : ctp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (75 of 78: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 44
  Gene deletion: b4467 b2242 b0469 b4269 b0493 b3588 b3003 b3011 b0474 b2518 b1241 b0351 b2744 b0871 b2781 b3617 b1004 b3713 b1109 b0046 b3236 b1612 b1611 b4122 b1759 b4374 b4161 b0675 b1415 b4138 b4123 b0621 b4381 b2406 b0452 b0114 b0529 b2492 b0904 b3028 b3918 b1912 b1206 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.387077 (mmol/gDw/h)
  Minimum Production Rate : 0.834274 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 992.136640
  EX_o2_e : 280.565124
  EX_glc__D_e : 10.000000
  EX_nh4_e : 7.452927
  EX_pi_e : 2.876199
  EX_so4_e : 0.097474
  EX_k_e : 0.075555
  EX_mg2_e : 0.003358
  EX_ca2_e : 0.002015
  EX_cl_e : 0.002015
  EX_cu2_e : 0.000274
  EX_mn2_e : 0.000267
  EX_zn2_e : 0.000132
  EX_ni2_e : 0.000125

Product: (mmol/gDw/h)
  EX_fe3_e : 999.993783
  EX_h2o_e : 550.264401
  EX_co2_e : 29.060178
  EX_succ_e : 1.033482
  EX_acald_e : 0.900109
  Auxiliary production reaction : 0.834274
  DM_oxam_c : 0.629581
  EX_thym_e : 0.070062
  DM_5drib_c : 0.000087
  DM_4crsol_c : 0.000086

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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