# =================================================================== # 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 SO:0000839_region /note /comment # ACT_SITE - Amino acid(s) involved in the activity of an enzyme. act_site SO:0001104_act_site /note /comment active_site_residue SO:0001104 /note /comment # BINDING - Binding site for any chemical group (co-enzyme, prosthetic # group, etc.). binding_site SO:0000409 /note /comment # CA_BIND - Extent of a calcium-binding region. ca_bind SO:0001094_ca_bind /note /comment ca_contact_site SO:0001094 /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 SO:0001089_carbohyd /note /comment # CHAIN - Extent of a polypeptide chain in the mature protein. chain SO:0000419_chain /note /comment mature_protein_region SO:0000419 /note /comment # COILED - Extent of a coiled-coil region coiled SO:0001080_coiled /note /comment coiled_coil SO:0001080 /note /comment # COMPBIAS - Extent of a compositionally biased region compbias SO:0001066_compbias /note /comment computationally_biased_region SO:0001066 /note /comment # CONFLICT - Different papers report differing sequences. # note usually begins MISSING or SEQ -> NEW (description optional) conflict SO:0001085_conflict /note /comment sequence_conflict SO:0001085 /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 SO:0001087_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 SO:0001088_disulfid /note /comment disulfide SO:0001088_disulfide /note /comment disulfide_bond SO:0001088 /note /comment # DNA_BIND - Extent of a DNA-binding region. DNA_bind SO:0000417_dna_bind /note /comment # DOMAIN - Extent of a domain of interest on the sequence. domain SO:0000417_domain /note /comment polypeptide_domain SO:0000417 /note /comment polypeptide_structural_domain SO:0001069 /note /comment # HELIX - DSSP secondary structure helix SO:0001117_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 SO:0000691_init_met /note /comment cleaved_initiator_methionine SO:0000691 /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 SO:0001090_lipid /note /comment # METAL - Binding site for a metal ion. metal SO:0001092_metal /note /comment metal_binding SO:0001092 /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 SO:0001089_mod_res /note /comment post_translational_modification SO:0001089 /note /comment # MOTIF - Short (up to 20 amino acids) sequence motif of biological interest motif SO:0001067_motif /note /comment polypeptide_motif SO:0001067 /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 SO:0001083_non_cons /note /comment non_adjacent_residues SO:0001083 /note /comment # NON_TER - The residue at an extremity of the sequence is not the terminal # residue. non_ter SO:0001084_non_ter /note /comment non_terminal_residue SO:0001084 /note /comment # NP_BIND - Extent of a nucleotide phosphate binding region. np_bind SO:0000409_np_bind /note /comment # PEPTIDE - Extent of a released active peptide. peptide SO:0001064_peptide /note /comment active_peptide SO:0001064 /note /comment # PROPEP - Extent of a propeptide. propep SO:0001062_propep /note /comment propeptide SO:0001062 /note /comment # REPEAT - Extent of an internal sequence repetition. repeat SO:0001068_repeat /note /comment polypeptide_repeat SO:0001068 /note /comment # SE_CYS - Selenocysteine se_cys /note /comment # SIGNAL - Extent of a signal sequence (prepeptide). signal SO:0000418_signal /note /comment signal_peptide SO:0000418 /note /comment # SIMILAR - Extent of a similarity with another protein sequence. similar /note /comment # SITE - Any other interesting site on the sequence. site SO:0000839_site /note /comment polypeptide_region SO:0000839 /note /comment # STRAND - DSSP secondary structure strand SO:0001111_strand /note /comment beta_strand SO:0001111 /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 SO:0001072_topo_dom /note /comment extramembrane SO:0001072 /note /comment # TRANSIT - Extent of a transit peptide (mitochondrial, chloroplastic, # cyanelle or for a microbody). transit SO:0000725_transit /note /comment transit_peptide SO:0000725 /note /comment # TRANSMEM - Extent of a transmembrane region. transmem SO:0001077_transmem /note /comment transmembrane SO:0001077 /note /comment # TURN - DSSP secondary structure turn SO:0001128 /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 SO:0001086_unsure /note /comment sequence_uncertainty SO:0001086 /note /comment # VARIANT - Authors report that sequence variants exist. # note usually begins MISSING or SEQ -> NEW (description optional) variant SO:0001147_variant /note /comment /ftid natural_variant SO:0001147 /note /comment /ftid # VARSPLIC - Description of sequence variants produced by alternative # splicing. varsplic /note /comment # ZN_FING - Extent of a zinc finger region. zn_fing SO:0000409_zn_fing /note /comment # Features from PIR feature tables with no match in SwissProt # Swissprot reports SIGNAL and PEPTIDE propeptide_cleavage_site SO:0001061 /note /comment cleavage_site SO:0001061_propeptide_cleavage_site /note /comment # Swissprot reports MOD_RES cross-link SO:0001087_cross-link /note /comment crosslink SO:0001087_crosslink /note /comment cross_link SO:0001087 /note /comment # Swissprot reports SITE with note INHIBITORY inhibitory_site /note /comment # Swissprot reports this in the description product /note /comment