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 (49 of 77: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 25
  Gene deletion: b4382 b3831 b4384 b3614 b0910 b4152 b2781 b0030 b3844 b1612 b1611 b4122 b0651 b2162 b1759 b4138 b4123 b0621 b2406 b3915 b0452 b2197 b3918 b4042 b1206   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.591890 (mmol/gDw/h)
  Minimum Production Rate : 0.311558 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 992.789612
  EX_o2_e : 268.456646
  EX_glc__D_e : 10.000000
  EX_nh4_e : 7.231843
  EX_pi_e : 0.882499
  EX_so4_e : 0.149050
  EX_k_e : 0.115533
  EX_mg2_e : 0.005135
  EX_ca2_e : 0.003081
  EX_cl_e : 0.003081
  EX_cu2_e : 0.000420
  EX_mn2_e : 0.000409
  EX_zn2_e : 0.000202
  EX_ni2_e : 0.000191
  EX_cobalt2_e : 0.000015

Product: (mmol/gDw/h)
  EX_fe3_e : 999.990494
  EX_h2o_e : 541.175512
  EX_co2_e : 22.211050
  EX_succ_e : 0.617219
  EX_ura_e : 0.419738
  Auxiliary production reaction : 0.311558
  DM_5drib_c : 0.000133
  DM_4crsol_c : 0.000132

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
Contact