Feature type and shape vocabulary

Every feature record has a type (see Load your own data). The viewer uses it to pick the feature’s default colour and shape from a table built into Nightingale, the library that draws the tracks. This page lists that table as shipped in @nightingale-elements/nightingale-track 5.11.1, the version the viewer draws with. It is generated from that package and kept in sync by drift tests, so it cannot silently diverge.

How a feature gets its colour and shape

The first of these that applies wins:

1. A colour or shape carried on the feature record itself. Some built-in kinds set one (InterPro domains get a colour per entry; PTMeXchange peptides are triangles); records from your own CSV, TSV or JSON file can set one with a color / shape column (or key); BED files cannot.
2. The track’s rendering.color and rendering.shape, set on the track or inherited from its group or from defaults:. These apply to every feature in the track, whatever its type.
3. The default for the feature’s type, from the table below.
4. black and rectangle.

Colour and shape are resolved separately, so a track can set one and keep the other.

type is matched without regard to case, against either the type code (ACT_SITE) or the UniProt name (active site) listed in the table.

Types ProtVista does not recognise

A type outside the table is drawn as a black rectangle. The viewer shows no error or warning; Nightingale only logs the type name to the browser console. Every unrecognised type looks the same, so a track that mixes two of them cannot tell them apart.

BED files have no type column, so every record read from a .bed file has type: BED and is drawn as a black rectangle unless its track sets rendering.

Worked example: a custom type

A lab marks its own hotspots with a type UniProt does not use:

type,start,end,description,score
HOTSPOT,132,140,Lab-defined mutational hotspot,0.87
HOTSPOT,601,612,Lab-defined mutational hotspot,0.64

On its own, each row draws as a black rectangle. Give the track a rendering block to choose the look instead:

accession: P05067
rows:
  - id: hotspots
    label: Hotspots
    kind: features
    data: ./hotspots.csv
    rendering:
      color: '#e67e22'
      shape: roundRectangle

Because rendering applies to the whole track, it also overrides the defaults of any recognised types in the same file. Keep custom types in their own file and track so the recognised ones keep their colours.

Recognised types

45 type codes, in the order Nightingale’s type table lists them.

Type	UniProt name	Label	Default shape	Default colour	Meaning
CHAIN	chain	Chain	rectangle	#CC9933	(aka mature region). This describes the extent of a polypeptide chain in the mature protein following processing
TRANSIT	transit peptide	Transit peptide	rectangle	#009966	This describes the extent of a transit peptide
INIT_MET	initiator methionine	Initiator methionine	arrow	#996633	This indicates that the initiator methionine is cleaved from the mature protein
PROPEP	propeptide	Propeptide	rectangle	#99CCCC	Part of a protein that is cleaved during maturation or activation
PEPTIDE	peptide	Peptide	rectangle	#006699	The position and length of an active peptide in the mature protein
SIGNAL	signal peptide	Signal peptide	rectangle	#CC0033	N-terminal signal peptide
HELIX	helix	Helix	rectangle	#FF0066	The positions of experimentally determined helical regions
STRAND	strand	Beta strand	rectangle	#FFCC00	The positions of experimentally determined beta strands
TURN	turn	Turn	rectangle	#0571AF	The positions of experimentally determined hydrogen-bonded turns
DISULFID	disulfide bond	Disulfide bond	bridge	#23B14D	The positions of cysteine residues participating in disulphide bonds
CROSSLNK	cross-link	Cross-link	bridge	#FF6600	Covalent linkages of various types formed between two proteins or between two parts of the same protein
REGION	region of interest	Region of interest	rectangle	#B33E00	Regions in multifunctional enzymes or fusion proteins, or characteristics of a region, e.g., protein-protein interactions mediation
COILED	coiled-coil region	Coiled-coil region	rectangle	#006699	Coiled coils are built by two or more alpha-helices that wind around each other to form a supercoil
MOTIF	short sequence motif	Short sequence motif	rectangle	#402060	Short conserved sequence motif of biological significance
REPEAT	repeat	Repeat	rectangle	#9900FF	Repeated sequence motifs or repeated domains within the protein
CA_BIND	calcium-binding region	Calcium-binding region	rectangle	#FF3399	Calcium-binding regions, such as the EF-hand motif
DNA_BIND	DNA-binding region	DNA binding	rectangle	#009933	DNA-binding domains such as AP2/ERF domain, the ETS domain, the Fork-Head domain, the HMG box and the Myb domain
DOMAIN	other domain of interest	Other domain of interest	rectangle	#9999FF	Specific combination of secondary structures organized into a characteristic three-dimensional structure or fold
ZN_FING	zinc finger region	Zinc finger	rectangle	#990066	Small, functional, independently folded domain that coordinates one or more zinc ions
NP_BIND	nucleotide-binding region	Nucleotide-binding region	rectangle	#FF9900	(aka flavin-binding). Region in the protein which binds nucleotide phosphates
METAL	metal ion-binding site	Metal ion-binding site	diamond	#009900	Binding site for a metal ion
SITE	other site of interest	Other site of interest	chevron	#660033	Any interesting single amino acid site on the sequence
BINDING	other binding site	Other binding site	rectangle	#009999	Binding site for any chemical group (co-enzyme, prosthetic group, etc.)
ACT_SITE	active site	Active site	circle	#FF6666	Amino acid(s) directly involved in the activity of an enzyme
MOD_RES	Post-translationally modified residue	Modified residue	triangle	#000066	Modified residues such as phosphorylation, acetylation, acylation, methylation
LIPID	lipid moiety-binding region	Lipidation	wave	#99CC33	Covalently attached lipid group(s)
CARBOHYD	glycosylation site	Glycosylation	hexagon	#CC3366	Covalently attached glycan group(s)
COMPBIAS	compositionally biased region	Compositionally biased region	rectangle	#FF3366	Position of regions of compositional bias within the protein and the particular amino acids that are over-represented within those regions
CONFLICT	sequence conflict	Sequence conflict	rectangle	#6633CC	Sequence discrepancies of unknown origin
NON_CONS	non-consecutive residues	Non-adjacent residues	doubleBar	#FF0033	Indicates that two residues in a sequence are not consecutive and that there is an undetermined number of unsequenced residues between them
NON_TER	non-terminal residue	Non-terminal residue	doubleBar	#339933	The sequence is incomplete. The residue is not the terminal residue of the complete protein
UNSURE	unsure residue	Sequence uncertainty	rectangle	#33FF00	Regions of a sequence for which the authors are unsure about the sequence assignment
NON_STD	non-standard amino acid	Non-standard residue	pentagon	#330066	Non-standard amino acids (selenocysteine and pyrrolysine)
MUTAGEN	mutagenesis site	Mutagenesis	rectangle	#FF9900	Site which has been experimentally altered by mutagenesis
TOPO_DOM	topological domain	Topological domain	rectangle	#CC0000	Location of non-membrane regions of membrane-spanning proteins
TRANSMEM	transmembrane region	Transmembrane	rectangle	#CC00CC	Extent of a membrane-spanning region
INTRAMEM	intramembrane region	Intramembrane	rectangle	#0000CC	Extent of a region located in a membrane without crossing it
VAR_SEQ	splice variant	Splice variant	rectangle	#CC11CC	—
VARIANT	sequence variant	Natural variant	circle	black	Natural variant of the protein, including polymorphisms, variations between strains, isolates or cultivars, disease-associated mutations and RNA editing events
UNIQUE	unique	Unique peptide	rectangle	#fc3133	—
NON_UNIQUE	non-unique	Non-unique peptide	rectangle	#8585fc	—
RESIDUE	residue	PTM residue	rectangle	#06038D	—
EPITOPE	epitope	Epitopes	rectangle	#4ade33	—
ANTIGEN	antigen	Antibody binding sequences	rectangle	#996699	—
PDBE_COVER	pdbe coverage	PDBe 3D structure coverage	rectangle	#669966	—

Shapes

rendering.shape takes one of these 22 names. The spellings (discontinuos) are Nightingale’s. Each is drawn below by the canvas track’s own drawing code: shapes that stretch across several residues, glyphs on one. 3 of them (leftEndedTag, rightEndedTag, doubleEndedTag) are declared but not drawn by the canvas track, and show a question mark instead. So does any other name: the config accepts any string for shape, and a misspelt one only shows up as a one-time warning naming it in the browser console.

Looks like	Shape	Drawn as	Default for
	rectangle	Stretches to cover the feature	CHAIN, TRANSIT, PROPEP, PEPTIDE, SIGNAL, HELIX, STRAND, TURN, REGION, COILED, MOTIF, REPEAT, CA_BIND, DNA_BIND, DOMAIN, ZN_FING, NP_BIND, BINDING, COMPBIAS, CONFLICT, UNSURE, MUTAGEN, TOPO_DOM, TRANSMEM, INTRAMEM, VAR_SEQ, UNIQUE, NON_UNIQUE, RESIDUE, EPITOPE, ANTIGEN, PDBE_COVER
	roundRectangle	Stretches to cover the feature	—
	bridge	Stretches to cover the feature	DISULFID, CROSSLNK
	line	Stretches to cover the feature	—
	diamond	Fixed-size glyph; across more than one residue a line joins its ends	METAL
	chevron	Fixed-size glyph; across more than one residue a line joins its ends	SITE
	catFace	Fixed-size glyph; across more than one residue a line joins its ends	—
	triangle	Fixed-size glyph; across more than one residue a line joins its ends	MOD_RES
	wave	Fixed-size glyph; across more than one residue a line joins its ends	LIPID
	hexagon	Fixed-size glyph; across more than one residue a line joins its ends	CARBOHYD
	pentagon	Fixed-size glyph; across more than one residue a line joins its ends	NON_STD
	circle	Fixed-size glyph; across more than one residue a line joins its ends	ACT_SITE, VARIANT
	arrow	Fixed-size glyph; across more than one residue a line joins its ends	INIT_MET
	doubleBar	Fixed-size glyph; across more than one residue a line joins its ends	NON_CONS, NON_TER
	discontinuosStart	Stretches to cover the feature	—
	discontinuos	Stretches to cover the feature	—
	discontinuosEnd	Stretches to cover the feature	—
	helix	Stretches to cover the feature	—
	strand	Stretches to cover the feature	—
	leftEndedTag	Not drawn — shows a question mark	—
	rightEndedTag	Not drawn — shows a question mark	—
	doubleEndedTag	Not drawn — shows a question mark	—