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 : dcamp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (59 of 77: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 35
  Gene deletion: b3399 b4382 b3942 b1732 b1241 b0351 b4069 b4384 b2744 b1479 b2297 b2458 b3617 b0160 b2407 b3844 b3236 b2463 b1982 b2210 b0675 b2361 b3551 b4219 b1832 b1778 b0114 b0529 b2492 b0904 b1710 b2480 b1511 b0606 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.413363 (mmol/gDw/h)
  Minimum Production Rate : 0.407077 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 27.560321
  EX_glc__D_e : 10.000000
  EX_nh4_e : 8.042381
  EX_pi_e : 0.805810
  EX_so4_e : 0.104093
  EX_k_e : 0.080686
  EX_fe2_e : 0.006639
  EX_mg2_e : 0.003586
  EX_ca2_e : 0.002152
  EX_cl_e : 0.002152
  EX_cu2_e : 0.000293
  EX_mn2_e : 0.000286
  EX_zn2_e : 0.000141
  EX_ni2_e : 0.000134
  EX_cobalt2_e : 0.000010

Product: (mmol/gDw/h)
  EX_h2o_e : 48.710664
  EX_co2_e : 25.794370
  EX_h_e : 10.105192
  EX_fum_e : 0.837072
  EX_thymd_e : 0.770798
  Auxiliary production reaction : 0.407077
  EX_ac_e : 0.240654
  EX_xan_e : 0.000278
  DM_mththf_c : 0.000185
  DM_5drib_c : 0.000093
  DM_4crsol_c : 0.000092

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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