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 (127 of 128: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 41
  Gene deletion: STM3646 STM1749 STM2463 STM2285 STM3526 STM0322 STM4326 STM1511 STM1884 STM0517 STM2947 STM3709 STM1135 STM2081 STM4183 STM0491 STM1326 STM4062 STM4408 STM1291 STM3069 STM4484 STM2317 STM3179 STM1480 STM4126 STM2338 STM2466 STM3241 STM0973 STM4467 STM2196 STM3240 STM2051 STM0007 STM2473 STM0402 STM0608 STM2971 STM1826 STM1341   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.066177 (mmol/gDw/h)
  Minimum Production Rate : 0.055876 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 9.078342
  EX_glc__D_e : 5.000000
  EX_nh4_e : 0.774731
  EX_pi_e : 0.114562
  EX_k_e : 0.011753
  EX_so4_e : 0.008072
  EX_mg2_e : 0.000522
  EX_fe2_e : 0.000484
  EX_ca2_e : 0.000313
  EX_cl_e : 0.000313
  EX_cobalt2_e : 0.000209
  EX_cu2_e : 0.000209
  EX_mn2_e : 0.000209
  EX_mobd_e : 0.000209
  EX_zn2_e : 0.000209

Product: (mmol/gDw/h)
  EX_h2o_e : 12.139316
  EX_co2_e : 9.975897
  EX_dha_e : 4.918379
  EX_h_e : 0.609787
  EX_acald_e : 0.168831
  Auxiliary production reaction : 0.055876
  EX_tyr__L_e : 0.045461
  EX_glyclt_e : 0.003309
  DM_hmfurn_c : 0.000030

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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