# ===================================================================
# 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 <modification> (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
