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 : ocdca_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (28 of 105: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 40
  Gene deletion: STM3646 STM2927 STM1749 STM2463 STM2285 STM3526 STM4570 STM4326 STM1511 STM1884 STM2947 STM3709 STM1135 STM4183 STM0370 STM1326 STM4062 STM2403 STM0393 STM4408 STM1291 STM3069 STM4484 STM2317 STM3179 STM1480 STM4126 STM3248 STM0519 STM1933 STM1124 STM3063 STM4467 STM2196 STM3240 STM0402 STM0608 STM2971 STM1826 STM1341   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.024037 (mmol/gDw/h)
  Minimum Production Rate : 0.081579 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 9.241371
  EX_glc__D_e : 5.000000
  EX_nh4_e : 0.320297
  EX_pi_e : 0.076720
  EX_k_e : 0.004269
  EX_so4_e : 0.002932
  EX_mg2_e : 0.000190
  EX_fe2_e : 0.000176
  EX_ca2_e : 0.000114
  EX_cl_e : 0.000114
  EX_cobalt2_e : 0.000076
  EX_cu2_e : 0.000076
  EX_mn2_e : 0.000076
  EX_mobd_e : 0.000076
  EX_zn2_e : 0.000076

Product: (mmol/gDw/h)
  EX_h2o_e : 11.521995
  EX_co2_e : 10.499210
  EX_dha_e : 4.883519
  EX_h_e : 0.397366
  Auxiliary production reaction : 0.081579
  EX_acald_e : 0.061325
  EX_kdo2lipid4_e : 0.027702
  EX_glyclt_e : 0.001202
  DM_hmfurn_c : 0.000011

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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