MetNetComp Database [1] / Core Genes

A set of core genes for simulation-based growth-coupled production. You can also see minimal gene deletions.

Model : STM_v1_0 [2].
Target metabolite : lipa_cold_c
Core genes for growth-coupled production (at least stoichioemetrically feasible)
  #Remaining genes : 294
  Remaining genes: STM1203 STM4122 STM2992 STM3795 STM3796 STM0320 STM1883 STM3190 STM4120 STM1712 STM3468 STM1067 STM2384 STM1195 STM4273 STM2378 STM1197 STM1198 STM3469 STM1824 STM0812 STM0488 STM0165 STM0203 STM0984 STM0207 STM1196 STM0483 STM2933 STM1232 STM4366 STM0730 STM2953 s0001 STM3710 STM0232 STM3379 STM3173 STM3380 STM4121 STM2366 STM4176 STM0533 STM2430 STM0534 STM0154 STM0737 STM0736 STM2432 STM2433 STM2431 STM1557 STM0380 STM0441 STM0442 STM0440 STM4247 STM0443 STM2555 STM0980 STM4300 STM3013 STM3947 STM3862 STM0222 STM3195 STM3923 STM0202 STM4235 STM0760 STM3740 STM3904 STM3700 STM0064 STM2489 STM0087 STM2365 STM1724 STM1723 STM3206 STM1058 STM0416 STM1163 STM3295 STM3486 STM1358 STM3719 STM1752 STM4123 STM1900 STM2098 STM2500 STM3539 STM3861 STM3877 STM3535 STM3722 STM4459 STM2649 STM3718 STM3717 STM4460 STM0002 STM1200 STM2641 STM0998 STM3692 STM1700 STM3713 STM2071 STM3926 STM3866 STM3869 STM3867 STM3865 STM3868 STM3871 STM1155 STM3864 STM3536 STM3870 STM4007 STM1889 STM2401 STM3314 STM4109 STM1299 STM2362 STM4131 STM0113 STM1777 STM2415 STM3909 STM0988 STM3316 STM1772 STM3880 STM3053 STM3054 STM3055 STM2167 STM4248 STM3200 STM0248 STM2510 STM0229 STM1467 STM1194 STM0045 STM0152 STM2193 STM1711 STM3359 STM0171 STM3721 STM3716 STM3712 STM3711 STM3723 STM3090 STM4115 STM3714 STM4114 STM3294 STM4221 STM2072 STM2074 STM1076 STM3938 STM0183 STM0003 STM2820 STM4182 STM2073 STM3724 STM1238 STM3715 STM1945 STM2443 STM2442 STM2444 STM2077 STM2441 STM2075 STM1725 STM2531 STM3903 STM3589 STM4105 STM2511 STM4414 STM0112 STM0110 STM0111 STM0372 STM2683 STM4119 STM2669 STM1310 STM2667 STM1349 STM4175 STM2078 STM2487 STM3001 STM2565 STM2076 STM4081 STM0645 STM1780 STM0978 STM0145 STM4348 STM2652 STM1727 STM1726 STM0226 STM0123 STM0228 STM3307 STM0128 STM0126 STM0129 STM4137 STM0756 STM1426 STM0417 STM0776 STM0124 STM3720 STM0134 STM2817 STM0218 STM3937 STM1707 STM2807 STM2808 STM0535 STM3114 STM3733 STM1617 STM0386 STM0310 STM1710 STM0125 STM2946 STM2934 STM2935 STM0153 STM2483 STM4465 STM3699 STM4466 STM3477 STM3401 STM0388 STM0166 STM0733 STM3624A STM0732 STM0735 STM0734 STM0738 STM0739 STM2473 STM2094 STM2096 STM2097 STM0985 STM0213 STM2082 STM2085 STM2086 STM2087 STM2083 STM1332 STM3905 STM2092 STM2091 STM2090 STM2093 STM0004 STM2089 STM2474 STM2232 STM2079 STM2838_S STM3290_S STM4188_S STM2499_S STM2105_S STM2549 STM2550 STM2548   (List of alternative genes)
  Computed by: AddGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.012124 (mmol/gDw/h)
  Minimum Production Rate : 0.013972 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 9.954275
  EX_glc__D_e : 5.000000
  EX_nh4_e : 0.161548
  EX_pi_e : 0.038693
  EX_k_e : 0.002153
  EX_so4_e : 0.001478
  EX_mg2_e : 0.000096
  EX_fe2_e : 0.000089
  EX_ca2_e : 0.000057
  EX_cl_e : 0.000057
  EX_cobalt2_e : 0.000038
  EX_cu2_e : 0.000038
  EX_mn2_e : 0.000038
  EX_mobd_e : 0.000038
  EX_zn2_e : 0.000038

Product: (mmol/gDw/h)
  EX_h2o_e : 11.357279
  EX_co2_e : 10.799515
  EX_dha_e : 4.941251
  EX_acald_e : 0.761629
  EX_h_e : 0.554523
  EX_ac_e : 0.395249
  Auxiliary production reaction : 0.013972
  EX_glyclt_e : 0.000606

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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