MetNetComp Database [1] / Minimal gene deletions

Minimal gene deletions for simulation-based growth-coupled production. You can also see maximal gene deletions.

Model : STM_v1_0 [2].
Target metabolite : pa160_p
List of minimal gene deletion strategies (Download)

Gene deletion strategy (123 of 128: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 39
  Gene deletion: STM1463 STM1749 STM2463 STM2285 STM3526 STM0322 STM4326 STM1885 STM2952 STM2947 STM3068 STM2141 STM1620 STM3597 STM0974 STM4408 STM1291 STM0518 STM4184 STM4484 STM0542 STM2317 STM3179 STM4569 STM1480 STM4126 STM4578 STM2338 STM2466 STM4467 STM3802 STM2196 STM3240 STM2051 STM0402 STM0608 STM3708 STM2971 STM1826   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.063341 (mmol/gDw/h)
  Minimum Production Rate : 0.055763 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 9.462454
  EX_glc__D_e : 5.000000
  EX_nh4_e : 0.700376
  EX_pi_e : 0.111934
  EX_k_e : 0.011249
  EX_so4_e : 0.007726
  EX_mg2_e : 0.000500
  EX_fe2_e : 0.000463
  EX_ca2_e : 0.000300
  EX_cl_e : 0.000300
  EX_cobalt2_e : 0.000200
  EX_cu2_e : 0.000200
  EX_mn2_e : 0.000200
  EX_mobd_e : 0.000200
  EX_zn2_e : 0.000200

Product: (mmol/gDw/h)
  EX_h2o_e : 12.219195
  EX_co2_e : 10.356772
  EX_dha_e : 4.936381
  EX_h_e : 0.542501
  EX_acald_e : 0.211755
  Auxiliary production reaction : 0.055763
  EX_glyclt_e : 0.003167
  EX_ade_e : 0.000472
  DM_hmfurn_c : 0.000028

Visualization
  1. Download JSON file.
  2. Go to Escher site [3].

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: 27-Sep-2023
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