| Step Name | Step Num | Required | Evidence (Method) | Evidence Go Terms |
|---|
| nonstructural protein NS3/small envelope | NS3_envE | YES | PF02723 (HMM): nonstructural protein NS3/Small envelope protein E | |
| coronavirus nonstructural protein NS1 | NSP1 | NO | PF06145 (HMM): coronavirus nonstructural protein NS1 | |
| replicase polyprotein NSP10 region | NSP10 | YES | PF09401 (HMM): RNA synthesis protein NSP10 | |
| coronavirus replicase polyprotein NSP11 region | NSP11 | YES | PF06471 (HMM): NSP11 | |
| replicase polyprotein NSP13 region | NSP13 | YES | PF06460 (HMM): coronavirus NSP13 | |
| coronavirus nonstructural protein NS2 | NSP2 | YES | PF04753 (HMM): coronavirus non-structural protein NS2 | |
| main protease | NSP3 | YES | PF05409 (HMM): coronavirus endopeptidase C30 | |
| replicase polyprotein NSP7 region | NSP7 | YES | PF08716 (HMM): nsp7 replicase | |
| replicase polyprotein NSP8 region | NSP8 | YES | PF08717 (HMM): nsp8 replicase | |
| replicase polyprotein NSP9 region | NSP9 | YES | PF08710 (HMM): nsp9 replicase | |
| papain-like protease | PLpro | YES | PF08715 (HMM): papain-like viral protease | |
| RNA-directed RNA Polymerase (N-terminal region) | RNA_pol | YES | PF06478 (HMM): coronavirus RPol N-terminal | |
| coronavirus M matrix/glycoprotein | coron_M | YES | PF01635 (HMM): coronavirus M matrix/glycoprotein | |
| corona nucleocapsid I protein | ncaps_I | YES | PF03187 (HMM): corona nucleocapsid I protein | |
| coronavirus nucleocapsid protein | ncapsid | YES | PF00937 (HMM): coronavirus nucleocapsid protein | |
| coronavirus S1 glycoprotein | spi_S1 | NO | PF01600 (HMM): coronavirus S1 glycoprotein | |
| coronavirus S2 glycoprotein | spi_S2 | YES | PF01601 (HMM): coronavirus S2 glycoprotein | |
