ProtVista

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• Interaction and customization
  • Zoom
  • Shapes and colors of features
  • Getting more information on track names and features
  • Customize
  • Natural variants track
• Feature categories and types

Interaction and customization

ProtVista presents sequence feature tracks under a ruler that represents sequence length for this protein. The track names are listed on the left hand side and the sequence features are shown in the horizontal track under the ruler.

You can expand a feature track to view all the sub-category titles by clicking on the blue area with the track name. In the example below, ‘Domains & Sites’ expands into ‘Domain’, ‘Binding site’, Active site’ and ‘Nucleotide binding site.

Zoom

You can zoom into a feature track right at various levels by double clicking on the feature you are interested, using your mouse zoom function or dragging the edges of the ruler into the area that you wish to zoom into. You can then slide the selected area on the ruler to focus on your area of interest.

You can directly zoom in to the level of the sequence (maximum possible zoom resolution) by clicking on the icon.

Shapes and colors of features

Sequence features that generally span multiple amino acids (like domains) are represented by rectangles. Other shapes represent sequence features that generally span only one amino acid. For example in the screenshot below, the purple rectangle represents a domain and the pink circle represents an active site. One track can have several sub-categories of features grouped inside it. Each feature sub-category has a dedicated color (for example ‘active site’ will have a different color to ‘binding site’).

Getting more information on track names and features

To learn more about a feature track’s name or or sub-category’s name and definition, hover over the title with your mouse.

To get more information about a sequence feature, click on it and you will see an info-box as shown below. You will also see a yellow highlight across the area occupied by the sequence feature so that you can easily see which other features overlap with it. Any selections can be reset by clicking on the white space in the tracks or by clicking on the icon.

Customize

You can customize the tracks that you see by clicking on the icon. You will see the list of all tracks with checkboxes to the left. You can deselect a checkbox in order to remove a track from view and select it to add the track back.

Natural variants track

The natural variants track shows natural variants from UniProt annotations as well as Large Scale Studies (COSMIC, 1000 Genomes, Exome Sequencing Project, ExAC). The default track view shows a summary chart indicating the number of variants at each sequence position. For example, the peaks show areas of high variation.

To expand the variants track and see all individual variants, click on the ‘Natural variants’ title area. You will now see each a chart where the x-axis consists of the sequence positions and the y-axis consists of all possible amino acids (shown below). All natural variants found for your protein are plotted on this chart, represented by colored circles. The variants are color coded by deleteriousness and source, with the exact legend shown on the left hand in the track title area.

You can filter the variants to see those curated by UniProt (UniProt Reviewed) or Large Scale Study variants. You can also filter by consequence and choose disease associated, predicted deleterious to predicted benign, non-disease associated and variants affecting the initiator codon, stop loss or stop gain.

Click on a variant to view more details about the variants including the exact sequence change, the evidence, source and identifiers.

Feature categories and types

Feature types are grouped in categories. Here we present the list of the currently supported feature categories and types.

Category name: DOMAIN_AND_SITES. Label: Domains & sites

Type	Label	Description	Shape
domain	Domain	Position and type of each modular protein domain	rectangle
repeat	Repeat	Positions of repeated sequence motifs or repeated domains	rectangle
ca_bind	Calcium binding	Position(s) of calcium binding region(s) within the protein	rectangle
zn_fing	Zinc finger	Position(s) and type(s) of zinc fingers within the protein	rectangle
dna_bind	DNA binding	Position and type of a DNA-binding domain	rectangle
np_bind	Nucleotide binding	Nucleotide phosphate binding region	rectangle
region	Region	Region of interest in the sequence	rectangle
coiled	Coiled coil	Positions of regions of coiled coil within the protein	rectangle
motif	Motif	Short (up to 20 amino acids) sequence motif of biological interest	rectangle
act_site	Active site	Amino acid(s) directly involved in the activity of an enzyme
metal	Metal binding	Binding site for a metal ion
binding	Binding site	Binding site for any chemical group (co-enzyme, prosthetic group, etc.)
site	Site	Any interesting single amino acid site on the sequence

Category name: MOLECULE_PROCESSING. Label: Molecule processing

Type	Label	Description	Shape
init_met	Initiator methionine	Cleavage of the initiator methionine
signal	Signal	Sequence targeting proteins to the secretory pathway or periplasmic space	rectangle
transit	Transit peptide	Extent of a transit peptide for organelle targeting	rectangle
propep	Propeptide	Part of a protein that is cleaved during maturation or activation	rectangle
chain	Chain	Extent of a polypeptide chain in the mature protein	rectangle
peptide	Peptide	Extent of an active peptide in the mature protein	rectangle

Category name: PTM. Label: Post translational modifications

Type	Label	Description	Shape
mod_res	Modified residue	Modified residues excluding lipids, glycans and protein cross-links
lipid	Lipidation	Covalently attached lipid group(s)
carbohyd	Glycosylation	Covalently attached glycan group(s)
disulfid	Disulfide bond	Cysteine residues participating in disulfide bonds
crosslnk	Cross-link	Residues participating in covalent linkage(s) between proteins

Category name: SEQUENCE_INFORMATION. Label: Sequence information

Type	Label	Description	Shape
compbias	Compositional biased	Region of compositional bias in the protein	rectangle
non_std	Non-standard residue	Occurrence of non-standard amino acids (selenocysteine and pyrrolysine) in the protein sequence
unsure	Sequence uncertainty	Regions of uncertainty in the sequence	rectangle
conflict	Sequence conflict	Description of sequence discrepancies of unknown origin	rectangle
non_cons	Non-adjacent residues	Indicates that two residues in a sequence are not consecutive
non_ter	Non-terminal residue	The sequence is incomplete. Indicate that a residue is not the terminal residue of the complete protein

Category name: STRUCTURAL. Label: Structural features

Category name: TOPOLOGY. Label: Topology

Category name: MUTAGENESIS. Label: Mutagenesis

Category name: PROTEOMICS. Label: Proteomics

Category name: VARIATION. Label: Variants