Appendix F - Appendix F to Subpart G of Part 1—List of Feature Keys Related to Protein Sequences
Source: World Intellectual Property Organization (WIPO) Handbook on Industrial Property Information and Documentation, Standard ST.25: Standard for the Presentation of Nucleotide and Amino Acid Sequence Listings in Patent Applications (2009).
| Key | Description | CONFLICT | different papers report differing sequences. | VARIANT | authors report that sequence variants exist. | VARSPLIC | description of sequence variants produced by alternative splicing. | MUTAGEN | site which has been experimentally altered. | MOD__RES | post-translational modification of a residue. | ACETYLATION | N-terminal or other. | AMIDATION | generally at the C-terminal of a mature active peptide. | BLOCKED | undetermined N- or C-terminal blocking group. | FORMYLATION | of the N-terminal methionine. | GAMMA-CARBOXYGLUTAMIC ACID HYDROXYLATION | of asparagine, aspartic acid, proline, or lysine. | METHYLATION | generally of lysine or arginine. | PHOSPHORYLATION | of serine, threonine, tyrosine, aspartic acid or histidine. | PYRROLIDONE CARBOXYLIC ACID | N-terminal glutamate which has formed an internal cyclic lactam. | SULFATATION | generally of tyrosine. | LIPID | covalent binding of a lipidic moiety. | MYRISTATE | myristate group attached through an amide bond to the N-terminal glycine residue of the mature form of a protein or to an internal lysine residue. | PALMITATE | palmitate group attached through a thioether bond to a cysteine residue or through an ester bond to a serine or threonine residue. | FARNESYL | farnesyl group attached through a thioether bond to a cysteine residue. | GERANYL-GERANYL | geranyl-geranyl group attached through a thioether bond to a cysteine residue. | GPI-ANCHOR | glycosyl-phosphatidylinositol (GPI) group linked to the alpha- carboxyl group of the C-terminal residue of the mature form of a protein. | N-ACYL DIGLYCERIDE | N-terminal cysteine of the mature form of a prokaryotic lipoprotein with an amide-linked fatty acid and a glyceryl group to which two fatty acids are linked by ester linkages. | DISULFID | disulfide bond; the `FROM' and `TO' endpoints represent the two residues which are linked by an intra-chain disulfide bond; if the `FROM' and `TO' endpoints are identical, the disulfide bond is an interchain one and the description field indicates the nature of the cross-link. | THIOLEST | thiolester bond; the `FROM' and `TO' endpoints represent the two residues which are linked by the thiolester bond. | THIOETH | thioether bond; the `FROM' and `TO' endpoints represent the two residues which are linked by the thioether bond. | CARBOHYD | glycosylation site; the nature of the carbohydrate (if known) is given in the description field. | METAL | binding site for a metal ion; the description field indicates the nature of the metal. | BINDING | binding site for any chemical group (co-enzyme, prosthetic group, etc.); the chemical nature of the group is given in the description field. | SIGNAL | extent of a signal sequence (prepeptide). | TRANSIT | extent of a transit peptide (mitochondrial, chloroplastic, or for a microbody). | PROPEP | extent of a propeptide. | CHAIN | extent of a polypeptide chain in the mature protein. | PEPTIDE | extent of a released active peptide. | DOMAIN | extent of a domain of interest on the sequence; the nature of that domain is given in the description field. | CA__BIND | extent of a calcium-binding region. | DNA__BIND | extent of a DNA-binding region. | NP__BIND | extent of a nucleotide phosphate binding region; the nature of the nucleotide phosphate is indicated in the description field. | TRANSMEM | extent of a transmembrane region. | ZN__FING | extent of a zinc finger region. | SIMILAR | extent of a similarity with another protein sequence; precise information, relative to that sequence, is given in the description field. | REPEAT | extent of an internal sequence repetition. | HELIX | secondary structure: Helices, for example, Alpha-helix, 3(10) helix, or Pi-helix. | STRAND | secondary structure: Beta-strand, for example, Hydrogen bonded beta-strand, or Residue in an isolated beta-bridge. | TURN | secondary structure Turns, for example, H-bonded turn (3-turn, 4-turn, or 5-turn). | ACT__SITE | amino acid(s) involved in the activity of an enzyme. | SITE | any other interesting site on the sequence. | INIT__MET | the sequence is known to start with an initiator methionine. | NON__TER | the residue at an extremity of the sequence is not the terminal residue; if applied to position 1, this signifies that the first position is not the N-terminus of the complete molecule; if applied to the last position, it signifies that this position is not the C-terminus of the complete molecule; there is no description field for this key. | NON__CONS | non consecutive residues; indicates that two residues in a sequence are not consecutive and that there are a number of unsequenced residues between them. | UNSURE | uncertainties in the sequence; used to describe region(s) of a sequence for which the authors are unsure about the sequence assignment. |
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