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 : 1odec11eg3p_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (113 of 113: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 40
  Gene deletion: STM3646 STM1749 STM2463 STM2285 STM3526 STM1290 STM4326 STM1511 STM1885 STM2952 STM0321 STM2947 STM3709 STM1135 STM4183 STM0491 STM1326 STM4062 STM4408 STM1291 STM4484 STM2317 STM3179 STM4569 STM1480 STM4126 STM4578 STM2338 STM2466 STM3241 STM0973 STM4467 STM2196 STM3240 STM2051 STM0402 STM0608 STM2971 STM1826 STM1341   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.069066 (mmol/gDw/h)
  Minimum Production Rate : 0.103902 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 9.097424
  EX_glc__D_e : 5.000000
  EX_nh4_e : 0.761108
  EX_pi_e : 0.165150
  EX_k_e : 0.012266
  EX_so4_e : 0.008425
  EX_mg2_e : 0.000545
  EX_fe2_e : 0.000506
  EX_cl_e : 0.000327
  EX_ca2_e : 0.000327
  EX_cobalt2_e : 0.000218
  EX_cu2_e : 0.000218
  EX_mn2_e : 0.000218
  EX_mobd_e : 0.000218
  EX_zn2_e : 0.000218

Product: (mmol/gDw/h)
  EX_h2o_e : 12.108760
  EX_co2_e : 9.996948
  EX_dha_e : 4.930631
  EX_h_e : 0.587235
  EX_acald_e : 0.176201
  Auxiliary production reaction : 0.103902
  EX_glyc__R_e : 0.001727
  DM_hmfurn_c : 0.000031

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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