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 : pg120_p
List of minimal gene deletion strategies (Download)

Gene deletion strategy (73 of 77: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 35
  Gene deletion: b2836 b0474 b2518 b2744 b3926 b4152 b2781 b1612 b1611 b4122 b2388 b1759 b0394 b1200 b3946 b0825 b4374 b4161 b0675 b2361 b2291 b4138 b4123 b0621 b0452 b0837 b0124 b2197 b3918 b4042 b1206 b2285 b3893 b1474 b4209   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.460554 (mmol/gDw/h)
  Minimum Production Rate : 0.188405 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 994.334402
  EX_o2_e : 279.889109
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.627143
  EX_pi_e : 0.632658
  EX_so4_e : 0.115977
  EX_k_e : 0.089897
  EX_mg2_e : 0.003995
  EX_ca2_e : 0.002397
  EX_cl_e : 0.002397
  EX_cu2_e : 0.000327
  EX_mn2_e : 0.000318
  EX_zn2_e : 0.000157
  EX_ni2_e : 0.000149
  EX_cobalt2_e : 0.000012

Product: (mmol/gDw/h)
  EX_fe3_e : 999.992603
  EX_h2o_e : 546.863978
  EX_co2_e : 32.215650
  EX_succ_e : 0.480262
  EX_ura_e : 0.326601
  Auxiliary production reaction : 0.188405
  EX_for_e : 0.001130
  DM_5drib_c : 0.000104
  DM_4crsol_c : 0.000103

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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