LiteFold/GO huggingface dataset:
peptidyl-L-3-phenyllactic acid biosynthetic process from peptidyl-phenylalanine (GO:0018061)
Namespace: biological_process
Definition: The modification of a N-terminal peptidyl-phenylalanine residue by either oxidative deamination or by transamination and subsequent reduction to form peptidyl-L-3-phenyllactic acid.
Synonyms: peptidyl-L-3-phenyllactic acid anabolism from peptidyl-phenylalanine; peptidyl-L-3-phenyllactic acid formation from peptidyl-phenylalanine; peptidyl-L-3-phenyllactic acid synthesis from peptidyl-phenylalanine
cytochrome c-heme linkage (GO:0018063)
Namespace: biological_process
Definition: The linkage of cytochromes and other heme proteins to heme.
Synonyms: cytochrome c-haem linkage
protein-L-histidine N-tele-methyltransferase activity (GO:0018064)
Namespace: molecular_function
Definition: Catalysis of the reaction: L-histidyl-[protein] + S-adenosyl-L-methionine = N(tele)-methyl-L-histidyl-[protein] + S-adenosyl-L-homocysteine.
Synonyms: actin-specific histidine methyltransferase activity; peptidyl-histidine N-methyltransferase activity; protein (histidine) methyltransferase activity; protein methylase IV activity; protein-histidine N-methyltransferase activity; S-adenosyl methionine:protein-histidine N-methyltransferase activity; S-adenosyl-L-methionine:protein-L-histidine N-tele-methyltransferase activity
obsolete protein-cofactor linkage (GO:0018065)
Namespace: biological_process
Definition: OBSOLETE. The covalent attachment of a cofactor to a protein.
Comment: 1. Making inferences in GO about compounds based on the cofactor role curated by ChEBI creates relationships that are not always true which violates ontological principles for GO; therefore we will cease making these inferences. 2. It is not meaningful to group protein modification processes that are not all chemically related by the fact that they may be used as a cofactor.
obsolete peptidyl-L-3',4'-dihydroxyphenylalanine biosynthetic process from peptidyl-tyrosine (GO:0018067)
Namespace: biological_process
Definition: OBSOLETE. The modification of protein tyrosine to peptidyl-L-3',4'-dihydroxyphenylalanine (DOPA).
Synonyms: peptidyl-L-3',4'-dihydroxyphenylalanine anabolism from peptidyl-tyrosine; peptidyl-L-3',4'-dihydroxyphenylalanine formation from peptidyl-tyrosine; peptidyl-L-3',4'-dihydroxyphenylalanine synthesis from peptidyl-tyrosine
Comment: This term was obsoleted because it represents a molecular function.
obsolete peptidyl-L-2',4',5'-topaquinone biosynthetic process from peptidyl-tyrosine (GO:0018068)
Namespace: biological_process
Definition: OBSOLETE. The modification of protein tyrosine to L-2',4',5'-topaquinone, characteristic of the active site of copper amine oxidases.
Synonyms: peptidyl-L-2',4',5'-topaquinone anabolism from peptidyl-tyrosine; peptidyl-L-2',4',5'-topaquinone formation from peptidyl-tyrosine; peptidyl-L-2',4',5'-topaquinone synthesis from peptidyl-tyrosine
Comment: This term was obsoleted because it represents a molecular function.
obsolete peptide cross-linking via 4'-(L-tryptophan)-L-tryptophyl quinone (GO:0018069)
Namespace: biological_process
Definition: OBSOLETE. The cross-linking of a tryptophan residue to tryptophyl quinone to form 4'-(L-tryptophan)-L-tryptophyl quinone, a cofactor found at the active site of methylamine dehydrogenase.
Comment: This term was obsoleted because it represents a cofactor, see PMID:2028257.
obsolete NAD(P)-cysteine ADP-ribosyltransferase activity (GO:0018071)
Namespace: molecular_function
Definition: OBSOLETE. Catalysis of the reaction: NAD(P)+ + L-cysteine = nicotinamide + N2-(ADP-D-ribosyl)-L-cysteine.
Comment: This term was obsoleted because it corresponds to the same reaction as NAD+- protein-cysteine ADP-ribosyltransferase activity ; GO:0140803.
obsolete peptidyl-L-glutamyl 5-glycerylphosphorylethanolamine biosynthetic process from peptidyl-glutamic acid (GO:0018072)
Namespace: biological_process
Definition: OBSOLETE. The modification of peptidyl-glutamic acid residues by the covalent attachment of ethanolamine, itself further modified by the addition of a phosphoglycerol unit.
Synonyms: peptidyl-L-glutamyl 5-glycerylphosphorylethanolamine anabolism from peptidyl-glutamic acid; peptidyl-L-glutamyl 5-glycerylphosphorylethanolamine formation from peptidyl-glutamic acid; peptidyl-L-glutamyl 5-glycerylphosphorylethanolamine synthesis from peptidyl-glutamic acid
Comment: This term was obsoleted because it represents a molecular function.
obsolete protein bromination (GO:0018073)
Namespace: biological_process
Definition: OBSOLETE. The addition of one or more bromine atoms to an amino acid residue in a protein.
Synonyms: protein amino acid bromination
N-terminal peptidyl-lysine acetylation (GO:0018076)
Namespace: biological_process
Definition: The acetylation of the N-terminal lysine of proteins.
obsolete protein iodination (GO:0018077)
Namespace: biological_process
Definition: OBSOLETE. The addition of one or more iodine atoms to an amino acid residue in a protein.
Synonyms: protein amino acid iodination
obsolete peptidyl-thyronine iodination (GO:0018078)
Namespace: biological_process
Definition: OBSOLETE. The iodination of peptidyl-thyronine, formed from tyrosine.
obsolete protein halogenation (GO:0018079)
Namespace: biological_process
Definition: OBSOLETE. The addition of a halogen to a protein amino acid.
Synonyms: protein amino acid halogenation
obsolete peptidyl-tryptophan bromination (GO:0018080)
Namespace: biological_process
Definition: OBSOLETE. The bromination of peptidyl-tryptophan, to form peptidyl-L-6'-bromotryptophan.
obsolete peptide cross-linking via lanthionine or 3-methyl-lanthionine (GO:0018081)
Namespace: biological_process
Definition: OBSOLETE. The synthesis of (2R,6R)-lanthionine, sn-(2S,6R)-lanthionine or (2S,3S,6R)-3-methyl-lanthionine, forming an intra-polypeptide cross-link between peptidyl-cysteine, and peptidyl-serine or peptidyl-threonine; dehydration of the serine or threonine residue to the alpha,beta-unsaturated amino acid is the first step; a bond then forms between the ethylene (ethene) group thus formed and the sulfur atom of a cysteine, with the inversion of the configuration of the alpha carbon of the serine or threonine occurring during the process.
Synonyms: peptide cross-linking via the thioethers lanthionine or 3-methyl-lanthionine; peptide cross-linking via the thiolethers lanthionine or 3-methyl-lanthionine
Comment: This term was obsoleted because it represents a molecular function; however the enzyme responsible for this reaction has not been defined in RESID.
obsolete peptidyl-(Z)-dehydrobutyrine biosynthetic process from peptidyl-threonine (GO:0018082)
Namespace: biological_process
Definition: OBSOLETE. The formation of (Z)-dehydrobutyrine by the dehydration of peptidyl-threonine.
Synonyms: peptidyl-(Z)-dehydrobutyrine anabolism from peptidyl-threonine; peptidyl-(Z)-dehydrobutyrine formation from peptidyl-threonine; peptidyl-(Z)-dehydrobutyrine synthesis from peptidyl-threonine
Comment: This term was obsoleted because it represents a molecular function.
peptidyl-L-3-oxoalanine biosynthetic process from peptidyl-cysteine or peptidyl-serine (GO:0018083)
Namespace: biological_process
Definition: The modification of peptidyl-cysteine or peptidyl-serine to peptidyl-L-3-oxoalanine; characteristic of the active sites of arylsulfatases.
Synonyms: peptidyl-L-3-oxoalanine anabolism from peptidyl-cysteine or peptidyl-serine; peptidyl-L-3-oxoalanine formation from peptidyl-cysteine or peptidyl-serine; peptidyl-L-3-oxoalanine synthesis from peptidyl-cysteine or peptidyl-serine
obsolete peptidyl-lactic acid biosynthetic process from peptidyl-serine (GO:0018084)
Namespace: biological_process
Definition: OBSOLETE. The modification of N-terminal peptidyl-serine to lactic acid.
Synonyms: peptidyl-lactic acid anabolism from peptidyl-serine; peptidyl-lactic acid formation from peptidyl-serine; peptidyl-lactic acid synthesis from peptidyl-serine
Comment: This term was obsoleted because it represents a molecular function.
obsolete peptidyl-L-amino acid racemization (GO:0018085)
Namespace: biological_process
Definition: OBSOLETE. The process of conversion of a L-amino acid into its enantiomer, the corresponding D-amino acid.
Comment: The reason for obsoletion is that this term represents a molecular function.
obsolete alanine racemization (GO:0018086)
Namespace: biological_process
Definition: OBSOLETE. (Was not defined before being made obsolete).
Synonyms: alanine racemization
Comment: This term was made obsolete because it was replaced with more appropriate terms.
protein polyglutamylation (GO:0018095)
Namespace: biological_process
Definition: The addition of one or more alpha-linked glutamyl units to the gamma carboxyl group of peptidyl-glutamic acid.
obsolete peptide cross-linking via S-(2-aminovinyl)-D-cysteine (GO:0018096)
Namespace: biological_process
Definition: OBSOLETE. The synthesis of (S,Z)-S-(2-aminovinyl)cysteine forming an intra-polypeptide cross-link between serine and cysteine.
Comment: This term was obsoleted because it represents a molecular function; however the enzyme responsible for this reaction has not been defined in RESID.
obsolete protein-chromophore linkage via peptidyl-S-4-hydroxycinnamyl-L-cysteine (GO:0018097)
Namespace: biological_process
Definition: OBSOLETE. The synthesis of the chromophore S-4-hydroxycinnamyl-L-cysteine.
Synonyms: protein amino acid cinnamylation
Comment: Term describes modified products or self-catalyzed processes.
obsolete protein citrullination (GO:0018101)
Namespace: biological_process
Definition: OBSOLETE. The hydrolysis of peptidyl-arginine to form peptidyl-citrulline.
Synonyms: deimination; peptidyl-citrulline anabolism from peptidyl-arginine; peptidyl-citrulline biosynthetic process from peptidyl-arginine; peptidyl-citrulline formation from peptidyl-arginine; peptidyl-citrulline synthesis from peptidyl-arginine
Comment: This term was obsoleted because it represents a molecular function.
obsolete peptidyl-arginine hydroxylation to peptidyl-4-hydroxy-L-arginine (GO:0018102)
Namespace: biological_process
Definition: OBSOLETE. The hydroxylation of peptidyl-arginine to form peptidyl-4-hydroxy-L-arginine.
Comment: This term was obsoleted because it represents a molecular function.
protein C-linked glycosylation (GO:0018103)
Namespace: biological_process
Definition: A protein glycosylation process in which a carbohydrate or carbohydrate derivative unit is added to a protein via a C atom.
Synonyms: protein amino acid C-linked glycosylation
peptidoglycan-protein cross-linking (GO:0018104)
Namespace: biological_process
Definition: The process of covalently linking peptidoglycan (murein) to proteins.
peptidyl-serine phosphorylation (GO:0018105)
Namespace: biological_process
Definition: The phosphorylation of peptidyl-serine to form peptidyl-O-phospho-L-serine.
peptidyl-threonine phosphorylation (GO:0018107)
Namespace: biological_process
Definition: The phosphorylation of peptidyl-threonine to form peptidyl-O-phospho-L-threonine.
peptidyl-tyrosine phosphorylation (GO:0018108)
Namespace: biological_process
Definition: The phosphorylation of peptidyl-tyrosine to form peptidyl-O4'-phospho-L-tyrosine.
peptidyl-arginine phosphorylation (GO:0018109)
Namespace: biological_process
Definition: The phosphorylation of peptidyl-arginine to form omega-N-phospho-L-arginine.
obsolete histone arginine kinase activity (GO:0018110)
Namespace: molecular_function
Definition: OBSOLETE. Catalysis of the reaction: histone L-arginine + ATP = histone N(omega)-phospho-L-arginine + ADP + 2 H+.
Synonyms: histone-arginine kinase activity
Comment: This term was obsoleted because it represents an unnecessary grouping class.
methionine racemase activity (GO:0018111)
Namespace: molecular_function
Definition: Catalysis of the reaction: L-methionine = D-methionine.
proline racemase activity (GO:0018112)
Namespace: molecular_function
Definition: Catalysis of the reaction: L-proline = D-proline.
lysine racemase activity (GO:0018113)
Namespace: molecular_function
Definition: Catalysis of the reaction: L-lysine = D-lysine.
threonine racemase activity (GO:0018114)
Namespace: molecular_function
Definition: Catalysis of the reaction: L-threonine = D-threonine.
obsolete peptidyl-S-diphytanylglycerol diether-L-cysteine biosynthetic process from peptidyl-cysteine (GO:0018115)
Namespace: biological_process
Definition: OBSOLETE. The modification of cysteine to form peptidyl-S-diphytanylglycerol diether-L-cysteine.
Synonyms: peptidyl-S-diphytanylglycerol diether-L-cysteine anabolism from peptidyl-cysteine; peptidyl-S-diphytanylglycerol diether-L-cysteine formation from peptidyl-cysteine; peptidyl-S-diphytanylglycerol diether-L-cysteine synthesis from peptidyl-cysteine
Comment: This term was obsoleted because it represents a molecular function.
obsolete peptidyl-lysine adenylylation (GO:0018116)
Namespace: biological_process
Definition: OBSOLETE. The adenylylation of peptidyl-lysine to form peptidyl-N6-(phospho-5'-adenosine)-L-lysine.
Synonyms: peptidyl-lysine adenylation
Comment: This term was obsoleted because it represents a molecular function.
protein adenylylation (GO:0018117)
Namespace: biological_process
Definition: The addition of an adenylyl group (adenosine 5'-monophosphate; AMP) to a protein amino acid.
Synonyms: protein adenylation; protein amino acid adenylylation; protein AMPylation
obsolete peptidyl-L-cysteine glutathione disulfide biosynthetic process from peptidyl-cysteine (GO:0018118)
Namespace: biological_process
Definition: OBSOLETE. The modification of peptidyl-cysteine by covalent addition of glutathione to form peptidyl-L-cysteine glutathione disulfide.
Synonyms: peptidyl-L-cysteine glutathione disulfide anabolism from peptidyl-cysteine; peptidyl-L-cysteine glutathione disulfide formation from peptidyl-cysteine; peptidyl-L-cysteine glutathione disulfide synthesis from peptidyl-cysteine; peptidyl-L-cysteine glutathione disulphide biosynthesis from peptidyl-cysteine; peptidyl-L-cysteine glutathione disulphide biosynthetic process from peptidyl-cysteine
Comment: This term was obsoleted because it represents a molecular function.
peptidyl-cysteine S-nitrosylation (GO:0018119)
Namespace: biological_process
Definition: The covalent addition of a nitric oxide (NO) group to the sulphur (S) atom of a cysteine residue in a protein, to form peptidyl-S-nitrosyl-L-cysteine.
Synonyms: protein S-nitrosylation; S-nitrosylation
obsolete peptidyl-arginine ADP-ribosylation (GO:0018120)
Namespace: biological_process
Definition: OBSOLETE. The transfer, from NAD, of ADP-ribose to peptidyl-arginine to form omega-N-(ADP-ribosyl)-L-arginine.
Comment: This term was obsoleted because it represents a molecular function.
obsolete NAD(P)-asparagine ADP-ribosyltransferase activity (GO:0018121)
Namespace: molecular_function
Definition: OBSOLETE. Catalysis of the reaction: NAD(P)+ + L-asparagine = nicotinamide + N2-(ADP-D-ribosyl)-L-asparagine.
Comment: This term was obsoleted because it doesn't correspond to a known reaction.
obsolete peptidyl-asparagine ADP-ribosylation (GO:0018122)
Namespace: biological_process
Definition: OBSOLETE. The transfer, from NAD, of ADP-ribose to peptidyl-asparagine to form peptidyl-N4-(ADP-ribosyl)-L-asparagine.
Comment: This term was obsoleted because it represents a molecular function.
obsolete peptidyl-cysteine ADP-ribosylation (GO:0018123)
Namespace: biological_process
Definition: OBSOLETE. The transfer, from NAD, of ADP-ribose to peptidyl-cysteine to form peptidyl-S-(ADP-ribosyl)-L-cysteine.
Comment: This term was obsoleted because it represents a molecular function.
obsolete peptide cross-linking via 5'-(N6-L-lysine)-L-topaquinone (GO:0018124)
Namespace: biological_process
Definition: OBSOLETE. The cross-linking of the epsilon-amino group of a peptidyl-lysine with peptidyl-topaquinone, a modified tyrosine residue.
Comment: This term was obsoleted because it represents a molecular function; however the enzyme responsible for this reaction has not been defined in RESID.
peptidyl-cysteine methylation (GO:0018125)
Namespace: biological_process
Definition: The methylation of peptidyl-cysteine to form peptidyl-S-methyl-L-cysteine.
obsolete NAD(P)-serine ADP-ribosyltransferase activity (GO:0018127)
Namespace: molecular_function
Definition: OBSOLETE. Catalysis of the reaction: NAD(P)+ + L-serine = nicotinamide + N2-(ADP-D-ribosyl)-L-serine.
Comment: This term was obsoleted because it represents the same reaction as NAD+-protein-serine ADP-ribosyltransferase activity ; GO:0140805.
obsolete peptidyl-serine cyclase activity (GO:0018128)
Namespace: molecular_function
Definition: OBSOLETE. (Was not defined before being made obsolete).
Synonyms: peptidyl-serine cyclase activity
Comment: This term was made obsolete because there is no record of why it was added, and no evidence can be found to suggest that this activity exists.
obsolete peptidyl-oxazoline dehydrogenase activity (GO:0018129)
Namespace: molecular_function
Definition: OBSOLETE. Catalysis of the reduction of a peptide-linked oxazoline to oxazole.
Comment: The reason for obsoletion is that it is not known to be catalyzed by any gene product.
obsolete heterocycle biosynthetic process (GO:0018130)
Namespace: biological_process
Definition: OBSOLETE. The chemical reactions and pathways resulting in the formation of heterocyclic compounds, those with a cyclic molecular structure and at least two different atoms in the ring (or rings).
Comment: The reason for obsoletion is that this term was an unnecessary grouping term.
obsolete oxazole or thiazole biosynthetic process (GO:0018131)
Namespace: biological_process
Definition: OBSOLETE. The chemical reactions and pathways resulting in the formation of oxazole or thiazole, five-membered heterocyclic ring structures containing an oxygen and a sulfur, respectively, in the 1-position and a nitrogen in the 3-position.
Synonyms: oxazole or thiazole anabolism; oxazole or thiazole biosynthesis; oxazole or thiazole formation; oxazole or thiazole synthesis
Comment: This term was obsoleted because it is an unnecessary grouping class.
obsolete peptide cross-linking via L-cysteine oxazolecarboxylic acid (GO:0018132)
Namespace: biological_process
Definition: OBSOLETE. The chemical reactions and pathways resulting in the formation of a peptidyl serine-peptidyl cysteine cross-link by the condensation of a serine hydroxyl with the carbonyl of the preceding residue and alpha-beta dehydrogenation.
Comment: This term was obsoleted because it represents a molecular function; however the enzyme responsible for this reaction has not been defined.
obsolete peptide cross-linking via L-cysteine oxazolinecarboxylic acid (GO:0018133)
Namespace: biological_process
Definition: OBSOLETE. The chemical reactions and pathways resulting in the formation of a peptidyl serine-peptidyl cysteine cross-link by the condensation of a serine hydroxyl with the carbonyl of the preceding residue.
Comment: This term was obsoleted because it represents a molecular function; however the enzyme responsible for this reaction has not been defined.
obsolete peptide cross-linking via glycine oxazolecarboxylic acid (GO:0018134)
Namespace: biological_process
Definition: OBSOLETE. The chemical reactions and pathways resulting in the formation of a peptidyl serine-peptidyl glycine cross-link by the condensation of a serine hydroxyl with the carbonyl of the preceding residue and alpha-beta dehydrogenation.
Comment: This term was obsoleted because it represents a molecular function; however the enzyme responsible for this reaction has not been defined.
obsolete peptidyl-cysteine cyclase activity (GO:0018135)
Namespace: molecular_function
Definition: OBSOLETE. (Was not defined before being made obsolete).
Synonyms: peptidyl-cysteine cyclase activity
Comment: This term was made obsolete because there is no record of why it was added, and no evidence can be found to suggest that this activity exists.
obsolete peptidyl-thiazoline dehydrogenase activity (GO:0018136)
Namespace: molecular_function
Definition: OBSOLETE. Catalysis of the reduction of a peptide-linked thiazoline to thiazole.
Comment: The reason for obsoletion is that it is not known to be catalyzed by any gene product.
obsolete peptide cross-linking via glycine thiazolecarboxylic acid (GO:0018137)
Namespace: biological_process
Definition: OBSOLETE. The chemical reactions and pathways resulting in the formation of a peptidyl cysteine-peptidyl glycine cross-link by the condensation of a cysteine thiol with the carbonyl of the preceding residue and alpha-beta dehydrogenation.
Comment: This term was obsoleted because it represents a molecular function; however the enzyme responsible for this reaction has not been defined.
obsolete peptide cross-linking via L-serine thiazolecarboxylic acid (GO:0018138)
Namespace: biological_process
Definition: OBSOLETE. The chemical reactions and pathways resulting in the formation of a peptidyl cysteine-peptidyl serine cross-link by the condensation of a cysteine thiol with the carbonyl of the preceding residue and alpha-beta dehydrogenation.
Comment: This term was obsoleted because it represents a molecular function; however the enzyme responsible for this reaction has not been defined.
obsolete peptide cross-linking via L-phenylalanine thiazolecarboxylic acid (GO:0018139)
Namespace: biological_process
Definition: OBSOLETE. The chemical reactions and pathways resulting in the formation of a peptidyl cysteine-peptidyl phenylalanine cross-link by the condensation of a cysteine thiol with the carbonyl of the preceding residue and alpha-beta dehydrogenation.
Comment: This term was obsoleted because it represents a molecular function; however the enzyme responsible for this reaction has not been defined.
obsolete peptide cross-linking via L-cysteine thiazolecarboxylic acid (GO:0018140)
Namespace: biological_process
Definition: OBSOLETE. The chemical reactions and pathways resulting in the formation of a peptidyl cysteine-peptidyl cysteine cross-link by the condensation of a cysteine thiol with the carbonyl of the preceding residue and alpha-beta dehydrogenation.
Comment: This term was obsoleted because it represents a molecular function; however the enzyme responsible for this reaction has not been defined.
obsolete peptide cross-linking via L-lysine thiazolecarboxylic acid (GO:0018141)
Namespace: biological_process
Definition: OBSOLETE. The chemical reactions and pathways resulting in the formation of a peptidyl cysteine-peptidyl lysine cross-link by the condensation of a cysteine thiol with the carbonyl of the preceding residue and alpha-beta dehydrogenation.
Comment: This term was obsoleted because it represents a molecular function; however the enzyme responsible for this reaction has not been defined.
obsolete protein-DNA covalent cross-linking (GO:0018142)
Namespace: biological_process
Definition: OBSOLETE. The formation of a covalent cross-link between DNA and a protein.
Synonyms: DNA-protein covalent cross-linking
Comment: The reason for obsoletion is that this term represents a molecular function.
obsolete protein-DNA covalent cross-linking via peptidyl-serine (GO:0018145)
Namespace: biological_process
Definition: OBSOLETE. The formation of a covalent cross-link between DNA and a peptidyl-serine residue by the formation of O-(phospho-5'-DNA)-L-serine.
Synonyms: DNA-protein covalent cross-linking via peptidyl-serine
Comment: The reason for obsoletion is that is not known to be catalyzed by any gene product.
keratan sulfate proteoglycan biosynthetic process (GO:0018146)
Namespace: biological_process
Definition: The chemical reactions and pathways resulting in the formation of keratan sulfate proteoglycans, which consist of a core protein linked to a keratan sulfate glycosaminoglycan. The keratan sulfate chain is composed of the repeating disaccharide unit beta-(1,4)-N-acetyl-D-glucosamine-beta-(1,3)-galactose, both of which can be sulfated. Keratan sulfate chains can be covalently linked either to an asparagine residue (N-linked) of the core protein via a high mannose oligasacccharide linker or to serine/threonine residues (O-linked) of the core protein via a core 2 type-linker.
Synonyms: keratan sulfate anabolism; keratan sulfate biosynthesis; keratan sulfate formation; keratan sulfate synthesis; keratan sulphate biosynthesis; keratan sulphate biosynthetic process