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 (41 of 105: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 48
  Gene deletion: STM3646 STM1749 STM2463 STM1220 STM1803 STM2285 STM3526 STM0192 STM2276 STM2477 STM4326 STM3614 STM1511 STM1884 STM2952 STM2947 STM3709 STM3068 STM2141 STM1135 STM4183 STM0491 STM0369 STM3597 STM0974 STM2403 STM4408 STM1291 STM4484 STM2317 STM3179 STM1480 STM3987 STM4126 STM0977 STM3661 STM1933 STM1124 STM3063 STM4467 STM2196 STM3240 STM1098 STM2022 STM0402 STM0608 STM2971 STM1826   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.017605 (mmol/gDw/h)
  Minimum Production Rate : 0.004809 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 10.567594
  EX_glc__D_e : 5.000000
  EX_nh4_e : 0.234559
  EX_pi_e : 0.056172
  EX_k_e : 0.003127
  EX_so4_e : 0.002148
  EX_mg2_e : 0.000139
  EX_fe2_e : 0.000129
  EX_cl_e : 0.000083
  EX_ca2_e : 0.000083
  EX_cu2_e : 0.000056
  EX_mn2_e : 0.000056
  EX_mobd_e : 0.000056
  EX_zn2_e : 0.000056
  EX_cobalt2_e : 0.000055

Product: (mmol/gDw/h)
  EX_h2o_e : 12.114125
  EX_co2_e : 11.365195
  EX_dha_e : 4.914724
  EX_acald_e : 0.753100
  EX_h_e : 0.230352
  EX_kdo2lipid4_e : 0.020280

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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