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 : pe140_p
List of minimal gene deletion strategies (Download)

Gene deletion strategy (76 of 77: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 38
  Gene deletion: b4467 b2836 b2242 b0474 b2518 b3831 b2781 b0030 b1004 b3713 b1109 b0046 b1612 b1611 b4122 b0651 b2162 b1759 b2210 b4161 b4138 b4123 b0621 b4381 b2406 b3915 b0306 b3605 b2492 b0904 b2197 b3028 b3918 b4042 b1695 b1206 b2285 b4209   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.467724 (mmol/gDw/h)
  Minimum Production Rate : 0.246642 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 25.914116
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.961391
  EX_pi_e : 0.697811
  EX_so4_e : 0.117783
  EX_k_e : 0.091296
  EX_fe3_e : 0.007514
  EX_mg2_e : 0.004058
  EX_ca2_e : 0.002435
  EX_cl_e : 0.002435
  EX_cu2_e : 0.000332
  EX_mn2_e : 0.000323
  EX_zn2_e : 0.000159
  EX_ni2_e : 0.000151
  EX_cobalt2_e : 0.000012

Product: (mmol/gDw/h)
  EX_h2o_e : 44.614235
  EX_co2_e : 29.380606
  EX_h_e : 5.698125
  EX_succ_e : 0.487739
  EX_ura_e : 0.331685
  Auxiliary production reaction : 0.246641
  EX_hxa_e : 0.000770
  DM_5drib_c : 0.000105
  DM_4crsol_c : 0.000104

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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