Sequence
Use this pane to color the molecule according to a pre-made sequence alignment.
Enter the sequence alignment:
Paste the aligned sequences (in FASTA or GDE format) into the
Alignment
text area below. If you include the solved sequence in this text area the identity and similarity calculations will include the solved sequence.
>Marmot p53 SSSVPSQNTYPGVYGFRLGFLHSGTAKSVTCTYSPSLNKLFCQLAKTCPV QLWVDSTPPPGTRVRAMAIYKKSQHMTEVVRRCPHHERCSDS-DGLAPPQ HLIRVEGNLRAEYLDDRNTFRHSVVVPYEPPEVGSECTTIHYNYMCNSSC MGGMNRRPILTIITLEGSSGNLLGRNSFEVRVCACPGRDRRTEEENF >Rat p53 SSSVPSQKTYQGNYGFHLGFLQSGTAKSVMCTYSISLNKLFCQLAKTCPV QLWVTSTPPPGTRVRAMAIYKKSQHMTEVVRRCPHHERCSDG-DGLAPPQ HLIRVEGNPYAEYLDDRQTFRHSVVVPYEPPEVGSDYTTIHYKYMCNSSC MGGMNRRPILTIITLEDSSGNLLGRDSFEVRVCACPGRDRRTEEENF >Hamster p53 SSSVPSYKTFQGDYGFRLGFLHSGTAKSVTCTYSPSLNKLFCQLAKTCPV QLWVNSTPPPGTRVRAMAIYKKLQYMTEVVRRCPHHERSSEG-DSLAPPQ HLIRVEGNLHAEYLDDKQTFRHSVVVPYEPPEVGSDCTTIHYNYMCNSSC MGGMNRRPILTIITLEDPSGNLLGRNSFEVRICACPGRDRRTEEKNF >Cat p53 SSFVPSQKTYPGAYGFHLGFLQSGTAKSVTCTYSPPLNKLFCQLAKTCPV QLWVRSPPPPGTCVRAMAIYKKSEFMTEVVRRCPHHERCPDSSDGLAPPQ HLIRVEGNLHAKYLDDRNTFRHSVVVPYEPPEVGSDCTTIHYNFMCNSSC MGGMNRRPIITIITLEDSNGKLLGRNSFEVRVCACPGRDRRTEEENF >Zebrafish p53 TSTVPETSDYPGDHGFRLRFPQSGTAKSVTCTYSPDLNKLFCQLAKTCPV QMVVDVAPPQGSVVRATAIYKKSEHVAEVVRRCPHHERTPDG-DNLAPAG HLIRVEGNQRANYREDNITLRHSVFVPYEAPQLGAEWTTVLLNYMCNSSC MGGMNRRPILTIITLETQEGQLLGRRSFEVRVCACPGRDRKTEESNF >Xenopus p53 SCAVPSTDDYAGKYGLQLDFQQNGTAKSVTCTYSPELNKLFCQLAKTCPL LVRVESPPPRGSILRATAVYKKSEHVAEVVKRCPHHERSVEPGEDAAPPS HLMRVEGNLQAYYMEDVNSGRHSVCVPYEGPQVGTECTTVLYNYMCNSSC MGGMNRRPILTIITLETPQGLLLGRRCFEVRVCACPGRDRRTEEDNY >Human p53 SSSVPSQKTYQGSYGFRLGFLHSGTAKSVTCTYSPALNKMFCQLAKTCPV QLWVDSTPPPGTRVRAMAIYKQSQHMTEVVRRCPHHERCSDS-DGLAPPQ HLIRVEGNLRVEYLDDRNTFRHSVVVPYEPPEVGSDCTTIHYNYMCNSSC MGGMNRRPILTIITLEDSSGNLLGRNSFEVRVCACPGRDRRTEEENL
Optional:
Enter the starting positions of the
Alignment
sequences separated by commas (to alter residue numbering in the reference alignment). An example entry is:
0,200,0,0
. If no numbers are given, the default starting position of 0 is used for each sequence.
91,91,93,85,61,67,93
Paste the aligned solved sequence into the
Solved Sequence
text area below (be sure to include the sequence title). You should load the molecule described by this sequence (using the
Molecule Control
pane) before continuing.
>Human p53 SSSVPSQKTYQGSYGFRLGFLHSGTAKSVTCTYSPALNKMFCQLAKTCPV QLWVDSTPPPGTRVRAMAIYKQSQHMTEVVRRCPHHERCSDS-DGLAPPQ HLIRVEGNLRVEYLDDRNTFRHSVVVPYEPPEVGSDCTTIHYNYMCNSSC MGGMNRRPILTIITLEDSSGNLLGRNSFEVRVCACPGRDRRTEEENL
Optional:
Enter the starting position of the
Solved Sequence
. This option can be used to alter residue numbering in the reference alignment, and to shift the color scheme on the solved structure (it may be necessary to shift the color scheme if the numbering in the PDB file differs from the alignment). An example entry is:
0
. If no number is entered the default starting position of 0 is used.
93
Choose the
colors
you want to use for highlighting. Indels (amino acids in the solved sequence that align with gaps in the other sequences) have the highest priority for coloring, followed by identical amino acids, and then similar amino acids.
The color of indels:
white
very light gray
light gray
medium gray
dark gray
very dark gray
black
lightest red
very light red
light red
medium red
dark red
very dark red
darkest red
lightest yellow
very light yellow
light yellow
medium yellow
dark yellow
very dark yellow
darkest yellow
lightest blue
very light blue
light blue
medium blue
dark blue
very dark blue
darkest blue
lightest green
very light green
light green
medium green
dark green
very dark green
darkest green
The color of identical amino acids:
white
very light gray
light gray
medium gray
dark gray
very dark gray
black
lightest red
very light red
light red
medium red
dark red
very dark red
darkest red
lightest yellow
very light yellow
light yellow
medium yellow
dark yellow
very dark yellow
darkest yellow
lightest blue
very light blue
light blue
medium blue
dark blue
very dark blue
darkest blue
lightest green
very light green
light green
medium green
dark green
very dark green
darkest green
The color of similar amino acids:
white
very light gray
light gray
medium gray
dark gray
very dark gray
black
lightest red
very light red
light red
medium red
dark red
very dark red
darkest red
lightest yellow
very light yellow
light yellow
medium yellow
dark yellow
very dark yellow
darkest yellow
lightest blue
very light blue
light blue
medium blue
dark blue
very dark blue
darkest blue
lightest green
very light green
light green
medium green
dark green
very dark green
darkest green
The percentage of sequences that must agree for indel, identical amino acid, or similar amino acid coloring to be added:
10
20
30
40
50
60
70
80
90
100
The color of divergent amino acids (amino acids that do not meet the threshold for indel, indentical amino acid, or similar amino acid coloring):
white
very light gray
light gray
medium gray
dark gray
very dark gray
black
lightest red
very light red
light red
medium red
dark red
very dark red
darkest red
lightest yellow
very light yellow
light yellow
medium yellow
dark yellow
very dark yellow
darkest yellow
lightest blue
very light blue
light blue
medium blue
dark blue
very dark blue
darkest blue
lightest green
very light green
light green
medium green
dark green
very dark green
darkest green
The default color (the color used for regions of the protein located outside of the sequence alignment):
white
very light gray
light gray
medium gray
dark gray
very dark gray
black
lightest red
very light red
light red
medium red
dark red
very dark red
darkest red
lightest yellow
very light yellow
light yellow
medium yellow
dark yellow
very dark yellow
darkest yellow
lightest blue
very light blue
light blue
medium blue
dark blue
very dark blue
darkest blue
lightest green
very light green
light green
medium green
dark green
very dark green
darkest green
Show labels on the molecule for
indels,
identical,
similar,
divergent residues.
Enter the groups of similar amino acids separated by commas to be used for the similarity calculation:
ILV,FWY,KRH,DE,GAS,P,C,TNQM
Use the following options to adjust the appearance of the reference alignment.
Show
100
90
80
70
60
50
40
30
residues per line.
Font style:
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Font size:
8
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24
36
Use colored
backgrounds
text
to highlight residues.