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 : ckdo_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (75 of 85: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 33
  Gene deletion: b3399 b0474 b2518 b2744 b4152 b0871 b2781 b0160 b1612 b1611 b4122 b1759 b4374 b4161 b0675 b2361 b2291 b4138 b4123 b0621 b0452 b0114 b0755 b3612 b0529 b2492 b0904 b3825 b3918 b0789 b1249 b1206 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.476600 (mmol/gDw/h)
  Minimum Production Rate : 0.251676 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 993.691529
  EX_o2_e : 283.688395
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.074875
  EX_pi_e : 0.711407
  EX_so4_e : 0.120017
  EX_k_e : 0.093029
  EX_mg2_e : 0.004135
  EX_ca2_e : 0.002481
  EX_cl_e : 0.002481
  EX_cu2_e : 0.000338
  EX_mn2_e : 0.000329
  EX_zn2_e : 0.000163
  EX_ni2_e : 0.000154
  EX_cobalt2_e : 0.000012

Product: (mmol/gDw/h)
  EX_fe3_e : 999.992345
  EX_h2o_e : 549.853212
  EX_co2_e : 33.826078
  EX_succ_e : 0.496995
  Auxiliary production reaction : 0.251676
  EX_ura_e : 0.086304
  DM_5drib_c : 0.000107
  DM_4crsol_c : 0.000106

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.

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Last updated: 21-Sep-2023
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