# =================================================================== # PROTEIN FEATURES # =================================================================== # Note # From the Swiss-Prot users manual # http://www.expasy.org/sprot/userman.html#FT_keys # Last checked 26 May 2006 # Many features are plain text with a final qualifier in brackets We # can represent these with /note plus a /comment for the part in # brackets. # We could also implement specific qualifiers for each special format # so we can parser the details for each feature, But what to do about # new GFF versions of the same features with possibly bad formatting? # REGION - Extent of a region of interest in the sequence region /note /comment # ACT_SITE - Amino acid(s) involved in the activity of an enzyme. act_site /note /comment # BINDING - Binding site for any chemical group (co-enzyme, prosthetic # group, etc.). binding /note /comment # CA_BIND - Extent of a calcium-binding region. ca_bind /note /comment # CARBOHYD - Glycosylation site. # This key describes the occurrence of the attachment of a glycan (mono- or # polysaccharide) to a residue of the protein: # # o The type of linkage (C- N- or O-linked) to the protein is indicated. # o If the nature of the reducing terminal sugar is known, its abbreviation # is shown between parenthesis. If three dots "..." follow the # abbreviation this indicates extension of the carbohydrate chain. # Conversely the absence of the dots indicate that a single monosaccharide # is linked. # Examples of CARBOHYD key feature lines: # # FT CARBOHYD 52 52 N-LINKED (GLCNAC...) (POTENTIAL). # FT CARBOHYD 162 162 O-LINKED (GLCNAC). # FT CARBOHYD 10 10 O-LINKED (GALNAC...) (BY SIMILARITY). # FT CARBOHYD 34 34 C-LINKED (MAN). carbohyd /note /comment # CHAIN - Extent of a polypeptide chain in the mature protein. chain /note /comment # COILED - Extent of a coiled-coil region coiled SO:0001080 /note /comment # COMPBIAS - Extent of a compositionally biased region compbias /note /comment # CONFLICT - Different papers report differing sequences. # note usually begins MISSING or SEQ -> NEW (description optional) conflict /note /comment # CROSSLNK - Posttranslationally formed amino acid bonds. # The 'FROM' and 'TO' endpoints designate the two residues, which are # linked by an intrachain bond, and the description field indicates # the nature of the cross-link. If the 'FROM' and 'TO' endpoints are # identical, the amino acid bond is an interchain one. The name of the # linked peptide is indicated in the description field. crosslnk /note /comment # 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. disulfid /note /comment # DNA_BIND - Extent of a DNA-binding region. dna_bind /note /comment # DOMAIN - Extent of a domain of interest on the sequence. domain /note /comment # HELIX - DSSP secondary structure helix /note /comment # INIT_MET - Initiator methionine. # This feature key is mostly associated with a zero value in the 'FROM' and # 'TO' fields to indicate that the initiator methionine has been cleaved off # and is not shown in the sequence: init_met /note /comment # LIPID - Covalent binding of a lipidic moiety # note is attached group name (optional comment) # known names are: #MYRISTATE Myristate group attached through an amide bond to the # N-terminal glycine residue of the mature form of a # protein [1,2] 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 [1,2] # #FARNESYL Farnesyl group attached through a thioether bond to a # cysteine residue [3,4] # #GERANYL-GERANYL Geranyl-geranyl group attached through a thioether bond # to a cysteine residue [3,4] # #GPI-ANCHOR Glycosyl-phosphatidylinositol (GPI) group linked to the # alpha-carboxyl group of the C-terminal residue of the # mature form of a protein [5,6] lipid /note /comment # METAL - Binding site for a metal ion. metal /note /comment # MOD_RES Post-translational modification of a residue. # note usually (description) # Most common codes are: #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 Of glutamate #HYDROXYLATION Of asparagine, aspartic acid, proline or lysine #METHYLATION Generally of lysine or arginine #PHOSPHORYLATION Of serine, threonine, tyrosine, aspartic acid # of histidine #PYRROLIDONE CARBOXYLIC ACID N-terminal glutamate which has formed an # internal cyclic lactam #SULFATATION Generally of tyrosine mod_res /note /comment # MOTIF - Short (up to 20 amino acids) sequence motif of biological interest motif /note /comment # MUTAGEN - Site which has been experimentally altered. # mutagen note usually SEQ ->NEW: description mutagen /note /comment # 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. non_cons /note /comment # NON_TER - The residue at an extremity of the sequence is not the terminal # residue. non_ter /note /comment # NP_BIND - Extent of a nucleotide phosphate binding region. np_bind /note /comment # PEPTIDE - Extent of a released active peptide. peptide /note /comment # PROPEP - Extent of a propeptide. propep /note /comment # REPEAT - Extent of an internal sequence repetition. repeat /note /comment # SE_CYS - Selenocysteine se_cys /note /comment # SIGNAL - Extent of a signal sequence (prepeptide). signal /note /comment # SIMILAR - Extent of a similarity with another protein sequence. similar /note /comment # SITE - Any other interesting site on the sequence. site /note /comment # STRAND - DSSP secondary structure strand /note /comment # THIOETH - Thioether bond. # The 'FROM' and 'TO' endpoints represent the two residues which are linked # by the thioether bond. thioeth /note /comment # THIOLEST - Thiolester bond. # The 'FROM' and 'TO' endpoints represent the two residues which are linked # by the thiolester bond. thiolest /note /comment # TOPO_DOM - Topological domain # New added 26-May-06 # Annotated with cellular component where domain is normally located # e.g. "Cytoplasmic" or "Mitochondrial matrix (potential)" topo_dom /note /comment # TRANSIT - Extent of a transit peptide (mitochondrial, chloroplastic, # cyanelle or for a microbody). transit /note /comment # TRANSMEM - Extent of a transmembrane region. transmem /note /comment # TURN - DSSP secondary structure turn /note /comment # UNSURE - Uncertainties in the sequence # Used to describe region(s) of a sequence for which the authors are unsure # about the sequence assignment. unsure /note /comment # VARIANT - Authors report that sequence variants exist. # replaced by VAR_SEQ, except for RNA editing recorded in the note variant /note /comment /ftid # VAR_SEQ - Description of sequence variants produced by alternative # splicing. var_seq /note /comment # ZN_FING - Extent of a zinc finger region. zn_fing /note /comment # Features from PIR feature tables with no match in SwissProt # Swissprot reports SIGNAL and PEPTIDE cleavage_site /note /comment # Swissprot reports MOD_RES cross-link /note /comment # Swissprot reports SITE with note INHIBITORY inhibitory_site /note /comment # Swissprot reports this in the description product note /comment