# =================================================================== # 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? # SITE - Any other interesting site on the sequence. polypeptide_region SO:0000839 SO:0000839_site SO:0000839_region SO:0000839_inhibitory_site /note /comment # ACT_SITE - Amino acid(s) involved in the activity of an enzyme. active_site_residue SO:0001104 SO:0001104_act_site /note /comment # BINDING - Binding site for any chemical group (co-enzyme, prosthetic # group, etc.). binding_site SO:0000409 SO:0100018_np_bind SO:0100020_zn_fing /note /comment # SO: # A region defined by its disposition to be involved in a biological process # used as a general feature by EMBOSS biological_region SO:0001411 epitope SO:0001018 /note /comment # CA_BIND - Extent of a calcium-binding region. ca_contact_site SO:0001094 SO:0001094_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). glycosylated_residue MOD:00693 /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 # coil: random coiled region of secondary structure e.g. predicted by # garnier algorithm coil SO:0100012 /note /comment # COILED - Extent of a coiled-coil region coiled_coil SO:0001080 /note /comment # COMPBIAS - Extent of a compositionally biased region computationally_biased_region SO:0001066 SO:0001066_compbias /note /comment # CONFLICT - Different papers report differing sequences. # note usually begins MISSING or SEQ -> NEW (description optional) #conflict SO:0001085 # /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 # /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. disulfide_bond SO:0001088 SO:0001088_disulfid SO:0001088_disulfide MOD:00034 /note /comment # DNA_BIND - Extent of a DNA-binding region. DNA_contact SO:0100020 /note /comment # DOMAIN - Extent of a domain of interest on the sequence. #domain SO:0000417 # /note # /comment polypeptide_domain SO:0000417 SO:0000417_dna_bind /note /comment polypeptide_structural_domain SO:0001069 /note /comment # HELIX - DSSP secondary structure alpha_helix SO:0001117 /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: 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] lipoconjugated_residue MOD:01155 /note /comment # METAL - Binding site for a metal ion. polypeptide_metal_contact SO:0001092 SO:0001092_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 post_translationally_modified_region SO:0001089 MOD:01156 /note /comment # MOTIF - Short (up to 20 amino acids) sequence motif of biological interest #motif SO:0001067_motif # /note # /comment polypeptide_motif SO:0001067 SO:0001067_motif /note /comment # MUTAGEN - Site which has been experimentally altered. # mutagen note usually SEQ ->NEW: description mutated_variant_site SO:0001148 /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_adjacent_residues SO:0001083 SO:0001083_non_cons /note /comment # NON_STD - non standard amino acid, used for pyrrolysine stop_codon_redefined_as_pyrrolysine SO:0000884 /note /comment # NON_TER - The residue at an extremity of the sequence is not the terminal # residue. non_terminal_residue SO:0001084 SO:0001084_non_ter /note /comment # NP_BIND - Extent of a nucleotide phosphate binding region. #np_bind SO:0100018_np_bind # /note # /comment # PEPTIDE - Extent of a released active peptide. active_peptide SO:0001064 SO:0001064_peptide /note /comment # PROPEP - Extent of a propeptide. propeptide SO:0001062 SO:0001062_propep /note /comment # REPEAT - Extent of an internal sequence repetition. polypeptide_repeat SO:0001068 SO:0001068_repeat /note /comment # SE_CYS - Selenocysteine stop_codon_redefined_as_selenocysteine SO:0000885 MOD:00031 /note /comment # SIGNAL - Extent of a signal sequence (prepeptide). signal_peptide SO:0000418 SO:0000418_signal /note /comment # SIMILAR - Extent of a similarity with another protein sequence. homologous SO:0000857 /note /comment # STRAND - DSSP secondary structure 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. thioether_crosslinked_residues MOD:00687 /note /comment # THIOLEST - Thiolester bond. # The 'FROM' and 'TO' endpoints represent the two residues which are linked # by the thiolester bond. thioester_crosslinked MOD:00395 /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)" extramembrane SO:0001072 SO:0001072_topo_dom /note /comment # TRANSIT - Extent of a transit peptide (mitochondrial, chloroplastic, # cyanelle or for a microbody). transit_peptide SO:0000725 SO:0000725_transit /note /comment # TRANSMEM - Extent of a transmembrane region. transmembrane SO:0001077 SO:0001077_transmem /note /comment # TURN - DSSP secondary structure polypeptide_turn_motif 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. 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_site SO:0001147 SO:0001147_variant /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 SO:0001061_propeptide_cleavage_site /note /comment #cleavage_site SO:0001061_propeptide_cleavage_site # /note # /comment # Swissprot reports MOD_RES cross_link SO:0001087 /note /comment # From PIR. Swissprot reports SITE with note INHIBITORY #inhibitory_site # /note # /comment # From PIR Swissprot reports this in the description #product # /note # /comment helix_turn_helix SO:0001081 /note /comment