When a portion of a protein sequence has been selected in any view (e.g., by double-clicking on a feature, or by dragging across the sequence with the mouse) except the Pairwise view, the Details panel contains the following information:
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- Sequence – The name of the sequence from which the region was selected.This is not shown for pairwise alignment selections.
- Alignment/Sequence selection – (Pairwise) Alignment selection displays the inclusive coordinates of the beginning and end of the selection.
When the sequence is not part of an alignment, (i.e., is listed with ‘unaligned sequences’), then Alignment selection is replaced with Sequence selection. In this case, the coordinates are the ungapped sequence coordinates rather than the alignment coordinates.
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Biophysical Properties
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Displays the physical properties of a continuous selection, including:
- MW [g/mol] – The molecular weight of the selected region.
- 1μg to pmol – The number of picomoles of protein in 1 microgram.
- Net charge (pH=7) – The pH-dependent sum of charges in a population of molecules. MegAlign Pro calculates the net charge for protein regions and amino acid residues, and assumes a pH of 7.
- pI – The isoelectric point (the pH at which the residue carries no net electrical charge), calculated from pKa tables from Lehninger et al. (2005). This calculation is available only for amino acid selections.
- Average hydropathy (GRAVY) – The Kyte-Doolittle hydropathy value, calculated using the method of Kyte, J. and Doolittle, R.F. (1982). This calculation is available only for amino acid selections.
- Aliphatic index – The relative volume occupied by aliphatic side chains (alanine, valine, isoleucine and leucine). This calculation is available only for amino acid selections and is made using the method of Gasteiger et al. (2005).
- Instability index – An estimate of the stability of the protein in a test tube. A protein whose instability index is smaller than 40 is predicted as stable, while a value above 40 predicts that the protein may be unstable. This value is calculated using the method of Guruprasad et al. (1990).
- 1 mg/mL to A280 – Calculates protein concentration from absorbance, where A280 is the absorbance (optical density) for the residue. This calculation is affected by presence of disulfide bonds, and assumes the disulfide bonds are oxidized (formed). This calculation is made using the method of Gasteiger et al. (2005).
- 1 mg/mL to A280 (red.) – Same as above, but assumes all disulfide bonds have been reduced (broken).
- A280 to 1 mg/mL – Calculates the absorbance of a protein concentration, where A280 is the absorbance (optical density) for the residue. This calculation is affected by presence of disulfide bonds and assumes the disulfide bonds are oxidized (formed). This calculation is made using the method of Gasteiger et al. (2005).
- A280 to 1 mg/mL (red.) – Same as above, but assumes all disulfide bonds have been reduced (broken).
- ε280 [M-¹cm-¹] – The extinction coefficient (amount of light a residue absorbs). This calculation assumes all Cys residues are reduced and all disulfide bonds are oxidized (formed). This calculation is available only for amino acid selections and is made using the method of Gasteiger et al. (2005).
- ε280 [M-¹cm-¹] (red.) – Same as above, but assumes all disulfide bonds have been reduced (broken).
Note: For aliphatic index, absorbance and extinction coefficient, the sequence is treated as independent residues. There is no algorithmic dependence on length.
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