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 : gdpmann_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (101 of 108: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 53
  Gene deletion: b3399 b4269 b3942 b1732 b0493 b3588 b3003 b3011 b1241 b0351 b2502 b2744 b1479 b0871 b3617 b3236 b0907 b1779 b2463 b3962 b1982 b0104 b2210 b4267 b4374 b0675 b2361 b2291 b1415 b3551 b1014 b0822 b4219 b1832 b1778 b0112 b2868 b0114 b0529 b1539 b2492 b0904 b3821 b1380 b0325 b1710 b2480 b0508 b4042 b4266 b1518 b1813 b4209   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.346962 (mmol/gDw/h)
  Minimum Production Rate : 0.459168 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 34.725356
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.463965
  EX_pi_e : 1.253017
  EX_so4_e : 0.087372
  EX_k_e : 0.067724
  EX_mg2_e : 0.003010
  EX_fe2_e : 0.002863
  EX_fe3_e : 0.002709
  EX_ca2_e : 0.001806
  EX_cl_e : 0.001806
  EX_cu2_e : 0.000246
  EX_mn2_e : 0.000240
  EX_zn2_e : 0.000118
  EX_ni2_e : 0.000112

Product: (mmol/gDw/h)
  EX_h2o_e : 51.069017
  EX_co2_e : 34.532542
  EX_h_e : 4.989359
  EX_acald_e : 1.413392
  Auxiliary production reaction : 0.459168
  EX_hxan_e : 0.105243
  EX_mththf_e : 0.105010
  DM_5drib_c : 0.000233
  EX_dxylnt_e : 0.000155
  DM_4crsol_c : 0.000077

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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