annotations, calculated attributes, family features, predictions, sequence annotation
Multiple Sequence Viewer/Editor — Annotations Pane
Select annotations to display for the sequences in the current tab.
To open this panel, click the Annotations button in the Multiple Sequence Viewer/Editor Panel.
- Overview
- Features
- Additional Resources
Overview of Annotations
Annotations are a means of representing additional information associated with the sequences. There are two classes of annotations: global annotations (e.g. consensus sequence, mean hydrophobicity) and local annotations. The global annotations are calculated for the entire set of sequences, the local annotations are computed for each sequence individually. Depending on the annotation type, they are presented as histogram plots (hydrophobicity, B-factor), color blocks (e.g. residue propensity), alphanumeric strings (consensus sequence, SSP, Pfam), graphical representations (secondary structure assignments).
There are two main tabs in the Annotations Pane: Quick Annotations and Calculated Attributes. The Quick Annotations tab contains Sequence annotations and Alignment annotations. The Calculated Attributes tab contains the Features and Predictions sections. The Annotations Settings are found at the bottom of the pane, and apply across both main tabs.
Annotations Pane Features
- Quick Annotations tab
- Contains Sequence annotations and Alignment annotations that can be computed rapidly and immediately displayed.
- Sequence annotations section
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The annotations in this section are local annotations.
- Disulfide Bonds
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Display disulfide bonds as lines connecting cysteine residues.
- Secondary Structure Assignment
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Display secondary structure assignment for the sequence. Double-clicking on this annotation will select all residues in the corresponding helix, strand, or loop.
- B-Factor
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Display histogram of temperature factors for each residue in the sequence.
- Binding Site
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Display a row in which residue positions are colored by the shortest distance between any ligand nonhydrogen atom and any nonhydrogen atom in the residue at that position. The menu which allows you to set the distance range used to detect contact becomes available when this annotation is toggled on. The default distance is 5Å. The colors are a heat map, with red meaning closest to the ligand and orange meaning slightly farther away. Red indicates the residue is within 1Å less than the specified distance. Orange indicates that it is within 1Å greater than the specified distance. The background color is used for residues outside of these ranges (not in binding site). You can select the binding-site residues for a particular ligand by right-clicking its row and choosing Select Associated Residues.
- Hydrophobicity
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Display histogram of Kyte-Doolittle hydrophobicity for each residue in the sequence. Hydrophobic residues have positive values; hydrophilic residues have negative values.
- Isoelectric Point
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Display histogram of isoelectric points in a 5-residue window. The isoelectric point of the isolated amino acid and the 5-residue window value are displayed in the tooltip for each histogram bar.
- Residue Numbers
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Display residue numbers below the sequence. The numbers are given every 5 residues, and are centered below the residue edges in the sequence. This is useful for tracking sequence changes after residue deletion, for example. The ruler only gives absolute alignments.
- Propensity
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Display a single row of color blocks that are colored according to one of a set of residue properties, chosen from the menu that is shown next to this item when it is selected. The properties are described under Color by option menu and information button in the reference, consensus, sequence coloring, color by, color carbons, transfer color, apply coloring. The row is presented like a sequence, but without letter codes, only the colors for the property.
The menu also includes a Helix Terminator item, which marks residues at the ends of helices, according to the following color scheme:
Scheme Residues Color Description GTMRKHF green helix-starting SNDELWP red helix-ending CQAVIY gray ambivalent - Antibody CDRs
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Display assignment of the three VL and VH regions. The residues are colored red, and a red line is displayed in the annotation for each region, labeled Ln or Hn for n = 1, 2, or 3. You can choose the numbering scheme from the menu that is shown next to this item when it is selected.
- Vernier Zone
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This option becomes available if Antibody CDRs is selected. Highlights the Vernier Zone residues in teal alongside selected Antibody CRDs annotations. The Vernier Zone menu has options for numbering schemes including Chothia, Enhanced Chothia, Kabat, IMGT, and AHo.
- Alignment annotations section
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The annotations in this section are global annotations.
- Consensus Sequence
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Display the consensus sequence at the top of the panel. The consensus sequence is the sequence that is composed of the most frequently occurring residue at each position in the sequence; if there are two residues that have the same frequency of occurrence, a + symbol is used, and the residues for this position are shown in its tooltip.
- Consensus Symbols
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Display a row at the top of the panel that contains symbols for the degree of consensus. The symbols follow the ClustalW conventions:
*Single, fully conserved residue. :One of the following "strong" groups is fully conserved: STA, NEQK, NHQK, NDEQ, QHRK, MILV, MILF, HY, FYW. .One of the following "weaker" groups is fully conserved: CSA, ATV, SAG, STNK, STPA, SGND, SNDEQK, NDEQHK, NEQHRK, FVLIM, HFY.
- Mean Hydrophobicity
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Display histogram of Kyte-Doolittle hydrophobicity for each residue in the alignment, averaged over all sequences. Hydrophobic residues have positive values; hydrophilic residues have negative values.
- Mean Isoelectric Point
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Display histogram of isoelectric points in a 5-residue window, averaged over all sequences. The isoelectric point of the isolated amino acid and the 5-residue window value are displayed in the tooltip for each histogram bar.
- Sequence Logo
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Display logo annotation. In this annotation, residue symbols at each position whose frequency of occurrence at that position is greater than a threshold are drawn in a vertical stack in order of frequency, with the height of the residue symbols proportional to the frequency of occurrence. (See Schneider T.D.; Stephens R.M. Sequence Logos: A New Way to Display Consensus Sequences. Nucleic Acids Res.1990, 18, 6097.) Hovering the mouse over this annotation will show a tooltip with the Conservation value: the value indicates the sequence conservation at that position, measured in bits. (See also Crooks GE, Hon G, Chandonia JM, Brenner SE. WebLogo: a sequence logo generator. Genome Res. 2004;14(6):1188-1190.)
- Calculated Attributes tab
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Contains Features and Predictions sections. Calculations must be run on the sequences before the annotations will display.
- Features section
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- Calculate Features link
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Select and compute family features for the specified sequences. Opens the Identify Family Features Dialog Box.
- Domains
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Perform analysis of selected sequences and predict boundaries of independently folding units within the protein.
- Family Features menu
- Display calculated features of supported protein families. Run a search on the protein family database, Pfam, to find families for the selected sequences, or for all sequences if no sequences are selected. The family options include Kinase Features, Kinase Binding Site Conservation, and GPCR Features
- Kinase Features
Display kinase features as a single row of color blocks that are colored according to the feature to which the residue belongs. The color scheme for these features is shown below. Each block has a tooltip identifying the residue and the feature it belongs to. The analysis to locate these features can take several minutes, during which Maestro and the MSV are unavailable.
Background Glycine Rich Loop ALPHA-C Gate Keeper Hinge Linker HRD Catalytic Loop DFG Activation Loop - Kinase Binding Site Conservation
Display a row of color blocks that are colored according to the conservation of residues in kinase binding sites. When you select this annotation, the kinase conservation is computed for the binding sites. This can take some time, and a message is displayed in the status bar of the MSV while the computation is in progress. The tooltip for the color block shows the residue identity and the conservation classification (as listed below with the color blocks).
VERY LOW LOW MEDIUM HIGH VERY HIGH - GPCR Features
Displays a row of color brackets that are colored according to GPCR values. The tooltip will show "GPCR value: [start] - [end]" where [start] is where this annotation residue starts in this segment, and [end] is where it ends, both labeled with the residue longcode and the residue number. The color-code for GPCR values is shown in the table below.
NTerm CTerm ICL1-3 ECL1-3 H8 TM1-8 Other - TCR Regions (T-Cell Receptor Regions)
Displays a row of color brackets that are colored according to T-Cell Receptor Regions. The tooltip will show "TCR Region: [start] - [end]" where [start] is where this annotation residue starts in this segment, and [end] is where it ends, both labeled with the residue longcode and the residue number. The color-code for T-Cell Receptor Regions types is shown in the table below.
A1, 2, 3 AFR1, 2, 3, 4 B1, 2, 3 BFR1, 2, 3, 4
- Predictions section
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- Run All Predictions link
- Run all of the predictions listed below. Opens the Run All Predictions Dialog Box.
- Secondary Structure
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Run the secondary structure programs to obtain a prediction of the secondary structure of the selected sequences, or of all sequences if no sequences are selected.
- Solvent Accessibility
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Predict accessibility of each residue to solvent. If more than 25% of total residue surface area is predicted to be exposed to the solvent, the residue is colored blue, otherwise it is colored yellow. Predicted items will be indicated with a hash fill pattern through the colored regions.
- Disulfide Bonds
- Display disulfide bonds as lines connecting cysteine residues, colored from black (strongest prediction) to light gray (weakest prediction).
- Disordered Regions
- Calculate a disorder score and classify residues by this score. The score is normalized to a 0 to 1 range. If a residue has a disorder score less than
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0.5, it is marked light gray. If the score is between 0.5 and 0.9, the residue is marked orange. If the score is greater than 0.9, the residue is marked red.
- Domain Arrangement
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Predict the arrangement of domains. Residues marked gray are likely to form a domain. Residues marked red are likely to be in linker (interdomain) regions.
- Annotation settings section
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Make settings for annotations which are applied across both the Quick Annotations and Calculated Attributes tabs.
- Group by Type option
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Display annotations separately from sequences, in groups. Each annotation group consists of the rows for a particular annotation for all sequences. The annotations in each group are in the same order as the sequences. This allows you to easily compare annotations across sequences.
If this option is deselected, annotations are listed underneath the sequence to which they belong.
- Clear All button
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Click to toggle off all annotations in the pane for all sequences. This action does not remove the calculated features data, and the annotations can be toggled on again. You can toggle off individual annotations by right-clicking on the annotation and choosing Clear Annotations. Note that this action will affect all sequences on the tab, not just the right-clicked sequence.