There are three types of proteins in coronaviruses: nonstructural, structural, and accessory proteins. Coronavirus proteins are essential for viral replication and for the binding and invasion of hosts and the regulation of host cell metabolism and immunity. This study investigated the amino acid sequence similarity and identity percentages of 10 proteins in SARS-CoV-2, SARS-CoV and the Rhinolophus affinis bat coronavirus (BatCoV RaTG13). The investigated proteins were the 1ab polyprotein, spike protein, orf3a, the envelope protein, the membrane protein, orf6, orf7a, orf7b, orf8, and the nucleocapsid protein. The online sequence alignment service of The European Molecular Biology Open Software Suite (EMBOSS) was used to determine the percentages of protein similarity and identity in the three viruses. The results showed that the similarity and identity percentages of the SARS-CoV-2 and BatCoV RaTG13 proteins were both greater than 95%, while the identity and similarity percentages of SARS-CoV-2 and SARS-CoV were both greater than 38%. The proteins of SARS-CoV-2 and BatCoV RaTG13 have high identity and similarity compared to those of SARS-CoV-2 and SARS-CoV. Graphic abstract The proteins of the SARS-CoV-2 are most identical and similar to those of BatCoV RaTG13 than to the proteins of SARS-CoV