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 : uri_p
List of minimal gene deletion strategies (Download)

Gene deletion strategy (40 of 41: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 44
  Gene deletion: b2242 b3553 b1478 b0474 b2518 b1241 b3831 b2930 b4232 b3697 b3925 b0871 b2297 b2458 b2926 b0030 b1004 b3713 b1109 b0046 b1612 b1611 b4122 b0651 b2162 b2690 b2210 b1033 b4161 b0675 b1415 b0411 b0822 b4138 b4123 b0621 b2913 b0114 b3028 b4042 b1206 b2285 b3893 b1474   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.359248 (mmol/gDw/h)
  Minimum Production Rate : 0.189735 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 990.250895
  EX_o2_e : 279.732271
  EX_glc__D_e : 10.000000
  EX_nh4_e : 4.389365
  EX_pi_e : 0.346533
  EX_so4_e : 0.090466
  EX_k_e : 0.070123
  EX_mg2_e : 0.003116
  EX_ca2_e : 0.001870
  EX_cl_e : 0.001870
  EX_cu2_e : 0.000255
  EX_mn2_e : 0.000248
  EX_zn2_e : 0.000123
  EX_ni2_e : 0.000116

Product: (mmol/gDw/h)
  EX_fe3_e : 999.994230
  EX_h2o_e : 543.241115
  EX_co2_e : 27.443649
  EX_pyr_e : 4.475455
  EX_for_e : 0.498817
  EX_succ_e : 0.374621
  EX_ac_e : 0.209149
  Auxiliary production reaction : 0.189735
  EX_ura_e : 0.065025
  EX_dxylnt_e : 0.000240
  DM_5drib_c : 0.000081
  DM_4crsol_c : 0.000080

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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