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 : grdp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (51 of 51: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 48
  Gene deletion: b4467 b1478 b3942 b1732 b1241 b0351 b2744 b3614 b0910 b4152 b0871 b2297 b2458 b2925 b2097 b2926 b3844 b1004 b3713 b1109 b0046 b1612 b1611 b4122 b2690 b2463 b2210 b4374 b0675 b2361 b2291 b3551 b1602 b4138 b4123 b0621 b4219 b1832 b1778 b2492 b0904 b1380 b1710 b2480 b1771 b1206 b0606 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.403369 (mmol/gDw/h)
  Minimum Production Rate : 0.106519 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 33.770674
  EX_glc__D_e : 10.000000
  EX_nh4_e : 4.356353
  EX_pi_e : 0.602130
  EX_so4_e : 0.101576
  EX_k_e : 0.078735
  EX_fe2_e : 0.006479
  EX_mg2_e : 0.003499
  EX_ca2_e : 0.002100
  EX_cl_e : 0.002100
  EX_cu2_e : 0.000286
  EX_mn2_e : 0.000279
  EX_zn2_e : 0.000138
  EX_ni2_e : 0.000130
  EX_cobalt2_e : 0.000010

Product: (mmol/gDw/h)
  EX_h2o_e : 46.239283
  EX_co2_e : 36.094848
  EX_h_e : 4.727107
  EX_12ppd__S_e : 1.247616
  EX_succ_e : 0.420630
  EX_3hpp_e : 0.286048
  Auxiliary production reaction : 0.106519
  DM_5drib_c : 0.000091
  DM_4crsol_c : 0.000090

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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