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 : pnto__R_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (61 of 79: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 39
  Gene deletion: b4467 b2836 b4382 b4384 b3708 b3008 b3752 b0871 b3115 b1849 b2296 b2925 b2097 b2407 b1004 b3713 b1109 b0046 b2690 b1982 b2797 b3117 b1814 b4471 b2210 b3945 b1602 b2406 b0114 b1539 b2492 b0904 b2578 b1533 b3927 b1380 b1511 b3662 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.447749 (mmol/gDw/h)
  Minimum Production Rate : 0.309122 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 28.838237
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.145074
  EX_pi_e : 0.431901
  EX_so4_e : 0.112752
  EX_k_e : 0.087397
  EX_fe2_e : 0.007191
  EX_mg2_e : 0.003884
  EX_ca2_e : 0.002331
  EX_cl_e : 0.002331
  EX_cu2_e : 0.000317
  EX_mn2_e : 0.000309
  EX_zn2_e : 0.000153
  EX_ni2_e : 0.000145
  EX_cobalt2_e : 0.000011

Product: (mmol/gDw/h)
  EX_h2o_e : 44.292240
  EX_co2_e : 28.355244
  EX_h_e : 8.227281
  EX_pyr_e : 3.494338
  Auxiliary production reaction : 0.309122
  DM_oxam_c : 0.000301
  DM_mththf_c : 0.000201
  DM_5drib_c : 0.000101
  DM_4crsol_c : 0.000100

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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