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 : ddca_p
List of minimal gene deletion strategies (Download)

Gene deletion strategy (58 of 76: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 25
  Gene deletion: b3831 b1278 b3614 b0910 b3752 b4152 b2781 b3236 b1612 b1611 b4122 b1638 b1759 b4138 b4123 b0621 b2913 b4381 b2406 b3736 b0452 b2197 b3029 b3918 b1206   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.241383 (mmol/gDw/h)
  Minimum Production Rate : 0.127446 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 14.938511
  EX_glc__D_e : 10.000000
  EX_nh4_e : 2.949270
  EX_pi_e : 0.232840
  EX_so4_e : 0.060785
  EX_k_e : 0.047116
  EX_fe2_e : 0.002315
  EX_mg2_e : 0.002094
  EX_fe3_e : 0.001562
  EX_ca2_e : 0.001256
  EX_cl_e : 0.001256
  EX_cu2_e : 0.000171
  EX_mn2_e : 0.000167
  EX_zn2_e : 0.000082
  EX_ni2_e : 0.000078

Product: (mmol/gDw/h)
  EX_h2o_e : 23.189705
  EX_h_e : 18.774105
  EX_co2_e : 15.708630
  EX_ac_e : 15.581394
  EX_succ_e : 0.251712
  EX_ura_e : 0.171176
  Auxiliary production reaction : 0.127446
  DM_5drib_c : 0.000054
  DM_4crsol_c : 0.000054

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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