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 : ttdca_p
List of minimal gene deletion strategies (Download)

Gene deletion strategy (100 of 109: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 28
  Gene deletion: b4382 b3831 b4384 b1278 b3614 b0910 b4152 b2297 b2458 b2781 b0767 b0030 b1232 b1612 b1611 b4122 b0651 b2162 b1759 b4138 b4123 b0621 b2406 b0452 b2197 b3918 b1206 b4209   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.543393 (mmol/gDw/h)
  Minimum Production Rate : 0.286454 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 987.336275
  EX_o2_e : 268.204226
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.639294
  EX_pi_e : 0.524160
  EX_so4_e : 0.136837
  EX_k_e : 0.106067
  EX_mg2_e : 0.004714
  EX_cl_e : 0.002828
  EX_ca2_e : 0.002828
  EX_cu2_e : 0.000385
  EX_mn2_e : 0.000375
  EX_zn2_e : 0.000185
  EX_ni2_e : 0.000176
  EX_cobalt2_e : 0.000014

Product: (mmol/gDw/h)
  EX_fe3_e : 999.991273
  EX_h2o_e : 538.350755
  EX_co2_e : 18.934583
  EX_succ_e : 3.144290
  EX_ura_e : 0.385346
  EX_ac_e : 0.316356
  Auxiliary production reaction : 0.286454
  DM_5drib_c : 0.000122
  DM_4crsol_c : 0.000121

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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