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 : ncam_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (100 of 116: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 32
  Gene deletion: b3553 b0474 b2518 b2744 b2930 b4232 b3697 b3925 b4152 b0871 b2779 b1612 b1611 b4122 b2690 b1033 b4374 b4161 b0675 b3945 b4388 b4138 b4123 b0621 b4381 b0114 b0509 b3125 b1206 b2285 b3893 b1474   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.381255 (mmol/gDw/h)
  Minimum Production Rate : 0.201358 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 986.128723
  EX_o2_e : 279.812678
  EX_glc__D_e : 10.000000
  EX_nh4_e : 4.658250
  EX_pi_e : 0.367761
  EX_so4_e : 0.096008
  EX_k_e : 0.074418
  EX_mg2_e : 0.003307
  EX_ca2_e : 0.001984
  EX_cl_e : 0.001984
  EX_cu2_e : 0.000270
  EX_mn2_e : 0.000263
  EX_zn2_e : 0.000130
  EX_ni2_e : 0.000123

Product: (mmol/gDw/h)
  EX_fe3_e : 999.993877
  EX_h2o_e : 539.906957
  EX_co2_e : 27.891380
  EX_for_e : 4.666915
  EX_ac_e : 4.359248
  EX_succ_e : 0.397569
  Auxiliary production reaction : 0.201358
  EX_ura_e : 0.069008
  DM_5drib_c : 0.000086
  DM_4crsol_c : 0.000085

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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