MetNetComp Database [1] / Core Genes

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

Model : iPC815 [2].
Target metabolite : adp_c
Core genes for growth-coupled production (at least stoichioemetrically feasible)
  #Remaining genes : 349
  Remaining genes: YPO3371 YPO1222 YPO0474 YPO3715 YPO3714 YPO3716 YPO2206 YPO2208 YPO0357 YPO0359 YPO0358 YPO1300 YPO3335 YPO2264 YPO3183 YPO4119 YPO2255 YPO2256 YPO1055 YPO0312 YPO3794 YPO1430 YPO3795 YPO3793 YPO0068 YPO3825 YPO3221 YPO2776 YPO1351 YPO1508 YPO2777 YPO1350 YPO1352 YPO1349 YPO1599 YPO1601 YPO1509 YPO2775 YPO2757 YPO2157 YPO2829 YPO3384 YPO3924 YPO4118 YPO1600 YPO1570 YPO3939 YPO3940 YPO2512 YPO2180 YPO2514 YPO1060 YPO0024 YPO3658 YPO3659 YPO3222 YPO2768 YPO3971 YPO2772 YPO3558 YPO1608 YPO2993 YPO2293 YPO1198 YPO2294 YPO1775 YPO0003 YPO0906 YPO2566 YPO0905 YPO0907 YPO4072 YPO1756 YPO1757 YPO0654 YPO1074 YPO2614 YPO2612 YPO2870 YPO2615 YPO3588 YPO3589 YPO2221 YPO2710 YPO1505 YPO2222 YPO1435 YPO1603 YPO1773 YPO3407 YPO1410 YPO0169 YPO2977 YPO3118 YPO3412 YPO2423 YPO1548 YPO1549 YPO3385 YPO1546 YPO0683 YPO0682 YPO4120 YPO4127 YPO4126 YPO4125 YPO4123 YPO4121 YPO4128 YPO4122 YPO1636 YPO3400 YPO0378 YPO1547 YPO3627 YPO1641 YPO3626 YPO3725 YPO1545 YPO1543 YPO0058 YPO2205 YPO3804 YPO0672 YPO3808 YPO3806 YPO3728 YPO3805 YPO3077 YPO3076 YPO3899 YPO3417 YPO2871 YPO0481 YPO0482 YPO1114 YPO0532 YPO1113 YPO0531 YPO0530 YPO4000 YPO0533 YPO4002 YPO2690 YPO4001 YPO4003 YPO2691 YPO1168 YPO1400 YPO2494 YPO3578 YPO2021 YPO2751 YPO1357 YPO2907 YPO3762 YPO2188 YPO1395 YPO2394 YPO0322 YPO2645 YPO2646 YPO1569 YPO1057 YPO1108 YPO3377 YPO3726 YPO1118 YPO1598 YPO3164 YPO3166 YPO3167 YPO3165 YPO3516 YPO0658 YPO3286 YPO0040 YPO1072 YPO1073 YPO3897 YPO0931 YPO0486 YPO2769 YPO0055 YPO1145 YPO3014 YPO3365 YPO0648 YPO3012 YPO1415 YPO1587 YPO3015 YPO1146 YPO0117 YPO3501 YPO1771 YPO0152 YPO2552 YPO2550 YPO1610 YPO2553 YPO0246 YPO2548 YPO3325 YPO3323 YPO3215 YPO2054 YPO3411 YPO2544 YPO2555 YPO2554 YPO2549 YPO3888 YPO3171 YPO2545 YPO2546 YPO2547 YPO2543 YPO1109 YPO1106 YPO1112 YPO1111 YPO1115 YPO1116 YPO0015 YPO0463 YPO2303 YPO3914 YPO1396 YPO0832 YPO3868 YPO3270 YPO2883 YPO0521 YPO1605 YPO0520 YPO2607 YPO4089 YPO0444 YPO3741 YPO3424 YPO3743 YPO3038 YPO3172 YPO3037 YPO3173 YPO0926 YPO0783 YPO3865 YPO0085 YPO0365 YPO1374 YPO3376 YPO2232 YPO3697 YPO2203 YPO2204 YPO0161 YPO1209 YPO1054 YPO4056 YPO3446 YPO1056 YPO2227 YPO3390 YPO3392 YPO3910 YPO2635 YPO0893 YPO0960 YPO0561 YPO0045 YPO1046 YPO0942 YPO3418 YPO3075 YPO4082 YPO2930 YPO4037 YPO4036 YPO1383 YPO2059 YPO1381 YPO3500 YPO2060 YPO3718 YPO0921 YPO1133 YPO2686 YPO3179 YPO2912 YPO1867 YPO2734 YPO1540 YPO2736 YPO1539 YPO2428 YPO2816 YPO1050 YPO3967 YPO2298 YPO3660 YPO4117 YPO3243 YPO3577 YPO4114 YPO4116 YPO1650 YPO1358 YPO3521 YPO2958 YPO2440 YPO1312 YPO2959 YPO2441 YPO2442 YPO1310 YPO0057 YPO0416 YPO3729 YPO2828 YPO0056 YPO4090 YPO1542 YPO3059 YPO2921 YPO1544 YPO2013 YPO1390 YPO0364 YPO3273 YPO0053 YPO1334 YPO1332 YPO1333 YPO2393 YPO1127 YPO2391 YPO3182 YPO0007 YPO3906 YPO3908 YPO3318 YPO3964 YPO2649 YPO2648 YPO3455 YPO0155 YPO0915   (List of alternative genes)
  Computed by: AddGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.013766 (mmol/gDw/h)
  Minimum Production Rate : 0.032700 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 8.578615
  EX_cit_e : 7.400000
  EX_h_e : 5.502988
  EX_glc__D_e : 2.000000
  EX_gly_e : 0.318325
  EX_pi_e : 0.076668
  EX_lys__L_e : 0.003442
  EX_phe__L_e : 0.002616
  EX_met__L_e : 0.001927
  EX_tyr__L_e : 0.001790
  EX_cys__L_e : 0.001005

Product: (mmol/gDw/h)
  EX_co2_e : 15.288164
  EX_h2o_e : 9.795444
  EX_succ_e : 7.400000
  EX_dha_e : 1.966024
  EX_pyr_e : 1.526544
  EX_ac_e : 0.410000
  Auxiliary production reaction : 0.032700
  EX_ade_e : 0.000096
  EX_glyc_e : 0.000073

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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