A method of ligation comprising the step of contacting an acyl donor compound of formula: wherein the transamidase recognition sequence is any peptide motif recognized by a transamidase enzyme; X is-O-, -NR-, or -S-; R is hydrogen, substituted or unsubstituted aliphatic, or substituted or unsubstituted heteroaliphatic; A 1 is acyl, substituted or unsubstituted aliphatic, substituted or unsubstituted heteroaliphatic, substituted or unsubstituted aryl, substituted or unsubstituted heteroaryl, a peptide, a protein, a polynucleotide, a carbohydrate, a tag, a metal atom, a contrast agent, a catalyst, a non-polypeptide polymer, a recognition element, a small molecule, a lipid, or a label; and R 1 is substituted or unsubstituted aliphatic, substituted or unsubstituted heteroaliphatic, substituted or unsubstituted aryl, or substituted or unsubstituted heteroaryl; with a nucleophilic compound of formula: wherein B 1 is acyl, substituted or unsubstituted aliphatic, substituted or unsubstituted heteroaliphatic, substituted or unsubstituted aryl, substituted or unsubstituted heteroaryl, a peptide, a protein, a polynucleotide, a carbohydrate, a tag, a metal atom, a contrast agent, a catalyst, a non-polypeptide polymer, a recognition element, a small molecule, a lipid, or a label; and n is an integer from 0 to 100, inclusive; in the presence of a transamidase enzyme under suitable conditions to form a compound of formula: wherein the recognition sequence is LPXT, wherein the X of the recognition sequence is any natural or unnatural amino acid, preferably wherein X is D, E, A, N, Q, K, or R; or wherein the recognition sequence is selected from LPXT, SPXT, LAXT, LSXT, NPXT, VPXT, IPXT and YPXR wherein the X of the recognition sequence is a natural or unnatural amino acid; or wherein the recognition sequence is selected from: LPKT, LPIT, LPDT, SPKT, LAET, LAAT, LAET, LAST, LAET, LPLT, LSRT, LPET, VPDT, IPQT, YPRR, LPMT, LPLT, LAFT, LPQT, NSKT, NPQT, NAKT, and NPQS; or wherein the recognition sequence is X 1 PX 2 X 3, where X 1 is leucine, isoleucine, valine or methionine, X 2 is any amino acid, X 3 is threonine, serine or alanine, P is proline, preferably wherein the transamidase is sortase A; or wherein the recognition sequence NPX 1 TX 2, where X 1 is glutamine or lysine, X 2 is asparagine or glycine, N is asparagine, P is proline and T is threonine, preferably wherein the transamidase is sortase B; and wherein when X is NR and R is H, R 1 is not CH 2 CO 2 H. the transamidase recognition sequence is any peptide motif recognized by a transamidase enzyme; X is-O-, -NR-, or -S-; R is hydrogen, substituted or unsubstituted aliphatic, or substituted or unsubstituted heteroaliphatic; A 1 is acyl, substituted or unsubstituted aliphatic, substituted or unsubstituted heteroaliphatic, substituted or unsubstituted aryl, substituted or unsubstituted heteroaryl, a peptide, a protein, a polynucleotide, a carbohydrate, a tag, a metal atom, a contrast agent, a catalyst, a non-polypeptide polymer, a recognition element, a small molecule, a lipid, or a label; and R 1 is substituted or unsubstituted aliphatic, substituted or unsubstituted heteroaliphatic, substituted or unsubstituted aryl, or substituted or unsubstituted heteroaryl; B 1 is acyl, substituted or unsubstituted aliphatic, substituted or unsubstituted heteroaliphatic, substituted or unsubstituted aryl, substituted or unsubstituted heteroaryl, a peptide, a protein, a polynucleotide, a carbohydrate, a tag, a metal atom, a contrast agent, a catalyst, a non-polypeptide polymer, a recognition element, a small molecule, a lipid, or a label; and n is an integer from 0 to 100, inclusive; wherein the recognition sequence is LPXT, wherein the X of the recognition sequence is any natural or unnatural amino acid, preferably wherein X is D, E, A, N, Q, K, or R; or wherein the recognition sequence is selected from LPXT, SPXT, LAXT, LSXT, NPXT, VPXT, IPXT and YPXR wherein the X of the recognition sequence is a natural or unnatural amino acid; or wherein the recognition sequence is selected from: LPKT, LPIT, LPDT, SPKT, LAET, LAAT, LAET, LAST, LAET, LPLT, LSRT, LPET, VPDT, IPQT, YPRR, LPMT, LPLT, LAFT, LPQT, NSKT, NPQT, NAKT, and NPQS; or wherein the recognition sequence is X 1 PX 2 X 3, where X 1 is leucine, isoleucine, valine or methionine, X 2 is any amino acid, X 3 is threonine, serine or alanine, P is proline, preferably wherein the transamidase is sortase A; or wherein the recognition sequence NPX 1 TX 2, where X 1 is glutamine or lysine, X 2 is asparagine or glycine, N is asparagine, P is proline and T is threonine, preferably wherein the transamidase is sortase B; and wherein when X is NR and R is H, R 1 is not CH 2 CO 2 H.