Species description | Species Name | Database term | Initial Amount |
---|---|---|---|
Native protein | NatP | N/A | 500 |
Misfolded protein | MisP | N/A | 0 |
Ubiquitin | Ub | IPR000626 | 500 |
Ubiquitin activating enzyme | E1 | IPR000011 | 100 |
Ubiquitin conjugating enzyme | E2 | IPR000608 | 100 |
Ubiquitin ligase (HECT) | E3 | IPR000569 | 100 |
De-ubiquitinating enzyme | DUB | IPR001394 | 200 |
Proteasome | Proteasome | GO:0000502 | 100 |
Reactive oxygen species | ROS | CHEBI:26523 | 10 |
Adenosine triphosphate | ATP | CHEBI:15422 | 10000 |
Adenosine diphosphate | ADP | CHEBI:16761 | 1000 |
Adenosine monophosphate | AMP | CHEBI:22254 | 1000 |
Misfolded protein bound by E3 | E3_MisP | IPR000569 | 0 |
E1 bound by Ub | E1_Ub | IPR000011 | 0 |
E2 bound by Ub | E2_Ub | IPR000608 | 0 |
Monoubiquitinated misfolded protein | MisP_Ub | IPR000626 | 0 |
Polyubiquitinated misfolded protein | MisP_Ub2, ... MisP_Ub8 | IPR000626 | 0 |
Polyubiquitinated protein bound to proteasome | MisP_Ub4_Proteasome ... MisP_Ub8_Proteasome | IPR000626 GO:0000502 | 0 |
Aggregated protein | AggP | N/A | 0 |
Sequestered aggregated protein | SeqAggP | N/A | 0 |
Aggregated protein bound to proteasome | AggP_Proteasome | GO:0000502 | 0 |
Dummy species to track chain length of substrate at degradation | degUb4, ..., degUb8 | N/A | 0 |