Macromolecular processes

Macromolecular machines catalyse the processes that produce, modify, and degrade macromolecules. They are associated with machine capacity constraints.

ID Name MachineSubunits ProcessComponents InitiationCofactors
P_SEC Secretion b3981: 1, b3300: 1, b0407: 1, b0408: 1, b3175: 1, b3705: 1, b0409: 1
A: {Products: {M_adp_c: 1.0, M_pi_c: 1.0}, Reactants: {M_atp_c: 1.0, M_h2o_c: 1.0}, Cost: 1.0}, C: {Products: {M_adp_c: 1.0, M_pi_c: 1.0}, Reactants: {M_atp_c: 1.0, M_h2o_c: 1.0}, Cost: 1.0}, D: {Products: {M_adp_c: 1.0, M_pi_c: 1.0}, Reactants: {M_atp_c: 1.0, M_h2o_c: 1.0}, Cost: 1.0}, E: {Products: {M_adp_c: 1.0, M_pi_c: 1.0}, Reactants: {M_atp_c: 1.0, M_h2o_c: 1.0}, Cost: 1.0}, F: {Products: {M_adp_c: 1.0, M_pi_c: 1.0}, Reactants: {M_atp_c: 1.0, M_h2o_c: 1.0}, Cost: 1.0}, G: {Products: {M_adp_c: 1.0, M_pi_c: 1.0}, Reactants: {M_atp_c: 1.0, M_h2o_c: 1.0}, Cost: 1.0}, H: {Products: {M_adp_c: 1.0, M_pi_c: 1.0}, Reactants: {M_atp_c: 1.0, M_h2o_c: 1.0}, Cost: 1.0}, I: {Products: {M_adp_c: 1.0, M_pi_c: 1.0}, Reactants: {M_atp_c: 1.0, M_h2o_c: 1.0}, Cost: 1.0}, K: {Products: {M_adp_c: 1.0, M_pi_c: 1.0}, Reactants: {M_atp_c: 1.0, M_h2o_c: 1.0}, Cost: 1.0}, L: {Products: {M_adp_c: 1.0, M_pi_c: 1.0}, Reactants: {M_atp_c: 1.0, M_h2o_c: 1.0}, Cost: 1.0}, M: {Products: {M_adp_c: 1.0, M_pi_c: 1.0}, Reactants: {M_atp_c: 1.0, M_h2o_c: 1.0}, Cost: 1.0}, N: {Products: {M_adp_c: 1.0, M_pi_c: 1.0}, Reactants: {M_atp_c: 1.0, M_h2o_c: 1.0}, Cost: 1.0}, P: {Products: {M_adp_c: 1.0, M_pi_c: 1.0}, Reactants: {M_atp_c: 1.0, M_h2o_c: 1.0}, Cost: 1.0}, Q: {Products: {M_adp_c: 1.0, M_pi_c: 1.0}, Reactants: {M_atp_c: 1.0, M_h2o_c: 1.0}, Cost: 1.0}, R: {Products: {M_adp_c: 1.0, M_pi_c: 1.0}, Reactants: {M_atp_c: 1.0, M_h2o_c: 1.0}, Cost: 1.0}, S: {Products: {M_adp_c: 1.0, M_pi_c: 1.0}, Reactants: {M_atp_c: 1.0, M_h2o_c: 1.0}, Cost: 1.0}, T: {Products: {M_adp_c: 1.0, M_pi_c: 1.0}, Reactants: {M_atp_c: 1.0, M_h2o_c: 1.0}, Cost: 1.0}, V: {Products: {M_adp_c: 1.0, M_pi_c: 1.0}, Reactants: {M_atp_c: 1.0, M_h2o_c: 1.0}, Cost: 1.0}, W: {Products: {M_adp_c: 1.0, M_pi_c: 1.0}, Reactants: {M_atp_c: 1.0, M_h2o_c: 1.0}, Cost: 1.0}, Y: {Products: {M_adp_c: 1.0, M_pi_c: 1.0}, Reactants: {M_atp_c: 1.0, M_h2o_c: 1.0}, Cost: 1.0}
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P_TA Translation
b4200: 1, b4203: 1, b4202: 1, b1716: 1, b1717: 1, b3983: 1, b3230: 1, b3310: 1, b3311: 1, b3316: 1, b3317: 1, b3314: 1, b3984: 1, rrnO-23S: 1, b3319: 1, b0023: 1, b3186: 1, b1211: 0, b3065: 1, b3165: 1, b3168: 0, b3231: 1, b0884: 0, b1480: 1, b2609: 1, b3320: 1, b0911: 1, b3637: 1, b3312: 1, b0170: 0, b3309: 1, b3308: 1, rrnO-5S: 1, b3636: 1, b3341: 1, b3321: 1, b3185: 1, b3342: 1, b3301: 1, b1089: 1, b3303: 1, b3302: 1, b3305: 1, b3304: 1, b3307: 1, b3306: 1, b3936: 1, b4147: 0, b3985: 1, b2606: 1, b3986: 4, b3315: 1, b3313: 1, b3340: 0, b2891: 0, b3299: 1, b3298: 1, b3297: 1, b3296: 1, b1718: 0, b3294: 1, b2185: 1, b0169: 1, b3703: 1, b3318: 1, rrnO-16S: 1, b3339: 5, M_gtp_c: 2, M_h2o_c: 2
A: {Products: {M_trnaala_c: 1.0, M_gdp_c: 2.0, M_pi_c: 2.0, M_h_c: 2.0}, Reactants: {M_alatrna_c: 1.0, M_gtp_c: 2.0, M_h2o_c: 2.0}, Cost: 1.0}, C: {Products: {M_trnacys_c: 1.0, M_gdp_c: 2.0, M_pi_c: 2.0, M_h_c: 2.0}, Reactants: {M_cystrna_c: 1.0, M_gtp_c: 2.0, M_h2o_c: 2.0}, Cost: 1.0}, D: {Products: {M_trnaasp_c: 1.0, M_gdp_c: 2.0, M_pi_c: 2.0, M_h_c: 2.0}, Reactants: {M_asptrna_c: 1.0, M_gtp_c: 2.0, M_h2o_c: 2.0}, Cost: 1.0}, E: {Products: {M_trnaglu_c: 1.0, M_gdp_c: 2.0, M_pi_c: 2.0, M_h_c: 2.0}, Reactants: {M_glutrna_c: 1.0, M_gtp_c: 2.0, M_h2o_c: 2.0}, Cost: 1.0}, F: {Products: {M_trnaphe_c: 1.0, M_gdp_c: 2.0, M_pi_c: 2.0, M_h_c: 2.0}, Reactants: {M_phetrna_c: 1.0, M_gtp_c: 2.0, M_h2o_c: 2.0}, Cost: 1.0}, G: {Products: {M_trnagly_c: 1.0, M_gdp_c: 2.0, M_pi_c: 2.0, M_h_c: 2.0}, Reactants: {M_glytrna_c: 1.0, M_gtp_c: 2.0, M_h2o_c: 2.0}, Cost: 1.0}, H: {Products: {M_trnahis_c: 1.0, M_gdp_c: 2.0, M_pi_c: 2.0, M_h_c: 2.0}, Reactants: {M_histrna_c: 1.0, M_gtp_c: 2.0, M_h2o_c: 2.0}, Cost: 1.0}, I: {Products: {M_trnaile_c: 1.0, M_gdp_c: 2.0, M_pi_c: 2.0, M_h_c: 2.0}, Reactants: {M_iletrna_c: 1.0, M_gtp_c: 2.0, M_h2o_c: 2.0}, Cost: 1.0}, K: {Products: {M_trnalys_c: 1.0, M_gdp_c: 2.0, M_pi_c: 2.0, M_h_c: 2.0}, Reactants: {M_lystrna_c: 1.0, M_gtp_c: 2.0, M_h2o_c: 2.0}, Cost: 1.0}, L: {Products: {M_trnaleu_c: 1.0, M_gdp_c: 2.0, M_pi_c: 2.0, M_h_c: 2.0}, Reactants: {M_leutrna_c: 1.0, M_gtp_c: 2.0, M_h2o_c: 2.0}, Cost: 1.0}, M: {Products: {M_trnamet_c: 1.0, M_gdp_c: 2.0, M_pi_c: 2.0, M_h_c: 2.0}, Reactants: {M_mettrna_c: 1.0, M_gtp_c: 2.0, M_h2o_c: 2.0}, Cost: 1.0}, N: {Products: {M_trnaasn_c: 1.0, M_gdp_c: 2.0, M_pi_c: 2.0, M_h_c: 2.0}, Reactants: {M_asntrna_c: 1.0, M_gtp_c: 2.0, M_h2o_c: 2.0}, Cost: 1.0}, P: {Products: {M_trnapro_c: 1.0, M_gdp_c: 2.0, M_pi_c: 2.0, M_h_c: 2.0}, Reactants: {M_protrna_c: 1.0, M_gtp_c: 2.0, M_h2o_c: 2.0}, Cost: 1.0}, Q: {Products: {M_trnagln_c: 1.0, M_gdp_c: 2.0, M_pi_c: 2.0, M_h_c: 2.0}, Reactants: {M_glntrna_c: 1.0, M_gtp_c: 2.0, M_h2o_c: 2.0}, Cost: 1.0}, R: {Products: {M_trnaarg_c: 1.0, M_gdp_c: 2.0, M_pi_c: 2.0, M_h_c: 2.0}, Reactants: {M_argtrna_c: 1.0, M_gtp_c: 2.0, M_h2o_c: 2.0}, Cost: 1.0}, S: {Products: {M_trnaser_c: 1.0, M_gdp_c: 2.0, M_pi_c: 2.0, M_h_c: 2.0}, Reactants: {M_sertrna_c: 1.0, M_gtp_c: 2.0, M_h2o_c: 2.0}, Cost: 1.0}, T: {Products: {M_trnathr_c: 1.0, M_gdp_c: 2.0, M_pi_c: 2.0, M_h_c: 2.0}, Reactants: {M_thrtrna_c: 1.0, M_gtp_c: 2.0, M_h2o_c: 2.0}, Cost: 1.0}, V: {Products: {M_trnaval_c: 1.0, M_gdp_c: 2.0, M_pi_c: 2.0, M_h_c: 2.0}, Reactants: {M_valtrna_c: 1.0, M_gtp_c: 2.0, M_h2o_c: 2.0}, Cost: 1.0}, W: {Products: {M_trnatrp_c: 1.0, M_gdp_c: 2.0, M_pi_c: 2.0, M_h_c: 2.0}, Reactants: {M_trptrna_c: 1.0, M_gtp_c: 2.0, M_h2o_c: 2.0}, Cost: 1.0}, Y: {Products: {M_trnatyr_c: 1.0, M_gdp_c: 2.0, M_pi_c: 2.0, M_h_c: 2.0}, Reactants: {M_tyrtrna_c: 1.0, M_gtp_c: 2.0, M_h2o_c: 2.0}, Cost: 1.0}, CHEBI:29108: {Products: {}, Reactants: {M_ca2_c: 1.0}, Cost: 0.0}, CHEBI:18420: {Products: {}, Reactants: {M_mg2_c: 1.0}, Cost: 0.0}, CHEBI:29105: {Products: {}, Reactants: {M_zn2_c: 1.0}, Cost: 0.0}, CHEBI:49883: {Products: {}, Reactants: {M_4fe4s_c: 1.0}, Cost: 0.0}, CHEBI:597326: {Products: {}, Reactants: {M_pydx5p_c: 1.0}, Cost: 0.0}, CHEBI:60240: {Products: {}, Reactants: {M_mg2_c: 1.0}, Cost: 0.0}, CHEBI:21137: {Products: {}, Reactants: {M_3fe4s_c: 1.0}, Cost: 0.0}, CHEBI:49786: {Products: {}, Reactants: {M_ni2_c: 1.0}, Cost: 0.0}, CHEBI:60539: {Products: {}, Reactants: {M_bmocogdp_c: 1.0}, Cost: 0.0}, CHEBI:57692: {Products: {}, Reactants: {M_fad_c: 1.0}, Cost: 0.0}, CHEBI:58937: {Products: {}, Reactants: {M_thmpp_c: 1.0}, Cost: 0.0}, CHEBI:30413: {Products: {}, Reactants: {M_pheme_c: 1.0}, Cost: 0.0}, CHEBI:29033: {Products: {}, Reactants: {M_fe2_c: 1.0}, Cost: 0.0}, CHEBI:60052: {Products: {}, Reactants: {M_sheme_c: 1.0}, Cost: 0.0}, CHEBI:58210: {Products: {}, Reactants: {M_fmn_c: 1.0}, Cost: 0.0}, CHEBI:29103: {Products: {}, Reactants: {M_k_c: 1.0}, Cost: 0.0}, CHEBI:23378: {Products: {}, Reactants: {M_cu2_c: 1.0}, Cost: 0.0}, CHEBI:83088: {Products: {}, Reactants: {M_lipoate_c: 1.0}, Cost: 0.0}, CHEBI:28115: {Products: {}, Reactants: {M_adocbl_c: 1.0}, Cost: 0.0}, CHEBI:49601: {Products: {}, Reactants: {M_2fe2s_c: 1.0}, Cost: 0.0}, CHEBI:24875: {Products: {}, Reactants: {M_fe2_c: 1.0}, Cost: 0.0}, CHEBI:29035: {Products: {}, Reactants: {M_mn2_c: 1.0}, Cost: 0.0}, CHEBI:47942: {Products: {}, Reactants: {M_pan4p_c: 1.0}, Cost: 0.0}, CHEBI:57540: {Products: {}, Reactants: {M_nad_c: 1.0}, Cost: 0.0}, CHEBI:15361: {Products: {}, Reactants: {M_pyr_c: 1.0}, Cost: 0.0}, CHEBI:57925: {Products: {}, Reactants: {M_gthrd_c: 1.0}, Cost: 0.0}, CHEBI:60344: {Products: {}, Reactants: {M_pheme_c: 1.0}, Cost: 0.0}, CHEBI:58442: {Products: {}, Reactants: {M_pqq_p: 1.0}, Cost: 0.0}, CHEBI:58349: {Products: {}, Reactants: {M_nadp_c: 1.0}, Cost: 0.0}, CHEBI:48828: {Products: {}, Reactants: {M_cobalt2_c: 1.0}, Cost: 0.0}, CHEBI:18408: {Products: {}, Reactants: {M_adocbl_c: 1.0}, Cost: 0.0}, CHEBI:57618: {Products: {}, Reactants: {M_fmnh2_c: 1.0}, Cost: 0.0}, CHEBI:17544: {Products: {}, Reactants: {M_hco3_c: 1.0}, Cost: 0.0}, CHEBI:71302: {Products: {}, Reactants: {M_bmoco1gdp_c: 1.0}, Cost: 0.0}, CHEBI:29101: {Products: {}, Reactants: {M_na1_c: 1.0}, Cost: 0.0}, CHEBI:29036: {Products: {}, Reactants: {M_cu2_c: 1.0}, Cost: 0.0}, CHEBI:24480: {Products: {}, Reactants: {M_hemeO_c: 1.0}, Cost: 0.0}, CHEBI:132124: {Products: {}, Reactants: {M_q8_c: 1.0}, Cost: 0.0}, CHEBI:17996: {Products: {}, Reactants: {M_cl_c: 1.0}, Cost: 0.0}, CHEBI:62814: {Products: {}, Reactants: {M_pheme_c: 1.0}, Cost: 0.0}, CHEBI:30408: {Products: {}, Reactants: {M_2fe2s_c: 1.0}, Cost: 0.0}, CHEBI:60342: {Products: {}, Reactants: {M_hmbil_c: 1.0}, Cost: 0.0}, CHEBI:79027: {Products: {}, Reactants: {M_tyr__L_c: 1.0}, Cost: 0.0}
1 M_fmettrna_c 1 M_gtp_c 2 M_h2o_c --> 1 M_trnamet_c 1 M_met__L_c 1 M_for_c 1 M_gdp_c 1 M_pi_c 1 M_h_c
P_CHP Folding b0436: 1, b0014: 1, b0015: 2, b4142: 7, b4143: 14, b2614: 2
A: {Products: {}, Reactants: {}, Cost: 0.1}, C: {Products: {}, Reactants: {}, Cost: 0.1}, D: {Products: {}, Reactants: {}, Cost: 0.1}, E: {Products: {}, Reactants: {}, Cost: 0.1}, F: {Products: {}, Reactants: {}, Cost: 0.1}, G: {Products: {}, Reactants: {}, Cost: 0.1}, H: {Products: {}, Reactants: {}, Cost: 0.1}, I: {Products: {}, Reactants: {}, Cost: 0.1}, K: {Products: {}, Reactants: {}, Cost: 0.1}, L: {Products: {}, Reactants: {}, Cost: 0.1}, M: {Products: {}, Reactants: {}, Cost: 0.1}, N: {Products: {}, Reactants: {}, Cost: 0.1}, P: {Products: {}, Reactants: {}, Cost: 0.1}, Q: {Products: {}, Reactants: {}, Cost: 0.1}, R: {Products: {}, Reactants: {}, Cost: 0.1}, S: {Products: {}, Reactants: {}, Cost: 0.1}, T: {Products: {}, Reactants: {}, Cost: 0.1}, V: {Products: {}, Reactants: {}, Cost: 0.1}, W: {Products: {}, Reactants: {}, Cost: 0.1}, Y: {Products: {}, Reactants: {}, Cost: 0.1}
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P_TSC Transcription
A: {Products: {M_ppi_c: 1.0, M_h_c: 1.0}, Reactants: {M_atp_c: 1.0, M_h2o_c: 1.0}, Cost: 0.0}, C: {Products: {M_ppi_c: 1.0, M_h_c: 1.0}, Reactants: {M_ctp_c: 1.0, M_h2o_c: 1.0}, Cost: 0.0}, G: {Products: {M_ppi_c: 1.0, M_h_c: 1.0}, Reactants: {M_gtp_c: 1.0, M_h2o_c: 1.0}, Cost: 0.0}, U: {Products: {M_ppi_c: 1.0, M_h_c: 1.0}, Reactants: {M_utp_c: 1.0, M_h2o_c: 1.0}, Cost: 0.0}
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P_REP Replication
A: {Products: {M_ppi_c: 1.0, M_h_c: 1.0}, Reactants: {M_datp_c: 1.0, M_h2o_c: 1.0}, Cost: 0.0}, C: {Products: {M_ppi_c: 1.0, M_h_c: 1.0}, Reactants: {M_dctp_c: 1.0, M_h2o_c: 1.0}, Cost: 0.0}, G: {Products: {M_ppi_c: 1.0, M_h_c: 1.0}, Reactants: {M_dgtp_c: 1.0, M_h2o_c: 1.0}, Cost: 0.0}, T: {Products: {M_ppi_c: 1.0, M_h_c: 1.0}, Reactants: {M_dttp_c: 1.0, M_h2o_c: 1.0}, Cost: 0.0}
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P_RNADEG RNA degradation
A: {Products: {M_amp_c: 1.0, M_h_c: 1.0}, Reactants: {M_h2o_c: 1.0}, Cost: 0.0}, C: {Products: {M_cmp_c: 1.0, M_h_c: 1.0}, Reactants: {M_h2o_c: 1.0}, Cost: 0.0}, G: {Products: {M_gmp_c: 1.0, M_h_c: 1.0}, Reactants: {M_h2o_c: 1.0}, Cost: 0.0}, U: {Products: {M_ump_c: 1.0, M_h_c: 1.0}, Reactants: {M_h2o_c: 1.0}, Cost: 0.0}
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test_process_1 Test process undefined