![]() After installation of the characteristic thioether cross-links, tailoring enzymes introduce additional post-translational modifications that are unique to each lanthipeptide and that fine-tune their activities and/or stability. The resulting polycyclic peptides have constrained conformations that confer their biological activities. In a cyclization process, Cys residues then attack the dehydrated residues to generate the lanthionine and methyllanthionine thioether cross-linked amino acids from which lanthipeptides derive their name. The post-translational modification reactions of lanthipeptides include dehydration of Ser and Thr residues to dehydroalanine and dehydrobutyrine, a transformation that is carried out in three unique ways in different classes of lanthipeptides. Lanthipeptides that display antimicrobial activity are called lantibiotics. Try the Clean Up button to remove numbers and other extraneous characters (preserves FASTA format).Lanthipeptides are ribosomally synthesized and post-translationally modified peptides (RiPPs) that display a wide variety of biological activities, from antimicrobial to antiallodynic. If a plain text protein sequence is entered, a map will be displayed showing all possible restriction sites allowed by back-translation of the sequence. The entire browser window (the result of a "select all") of a GenBank/ENA/DDBJ page can be pasted into the text box. Supported Formats The supported formats include DDBJ, ENA, GCG, GenBank, FASTA and plain text. To add auto-annotation to GenBank/ENA/DDBJ pages, the Tags/Orfs box must be checked as well. Orfs and tags are detected by default in plain text input.Īnnotate If checked, open reading frames will be annotated automatically. Tags/Orfs If checked, open reading frames and common peptide tags will be identified in DDBJ/ENA/GenBank pages. Unannotated sequences will be converted to circular if a plasmid is detected. #9a80ff, can be entered (the hexadecimal digits are 0-9a-f).ĭefault If selected, an archive format sequence will be displayed as specified by the input. ![]() Any red green blue hexadecimal code of the form #rrggbb, e.g. #9a80ff, can be entered (the hexadecimal digits are 0-9a-f).Īmino Acids: Sets the color of the amino acid links. Unique Sites: Sets the color used to display sites that appear only once in the sequence. Page Background Sets the background color of the page. Whatever is entered will be repeated throughout the sequence. Separator Template: Creates a custom separator between the top and bottom lines of the displayed sequence. Sequence Width: Sets the number of basepairs displayed per line. Minimum Orf Length: Requires open reading frames to have a minimum length. The application does not attempt to identify open reading frames in ENA/DDBJ/GenBank pages unless gb+ or the Tags/Orfs checkbox at the right top of the sequence box is checked.Īllowed Overlap: Allows orfs to overlap by this number of basepairs without causing rejection. Reject Overlapping Orfs: Allows or prevents the display of overlapping open reading frames.įrames Wanted These checkboxes allow various reading frames to be shown. A choice to capture additional bacterial orfs might be MVIL. Start Residues: Amino acid codons allowed at the beginning of an open reading frame. The file must have the same structure as the file "enzymeData" in subfolder /enz/ of this site. Enzymes can also be added to the text field directly.Įnzyme File: Can be used to provide a local file containing data on the enzymes to be used. To display only specific enzymes, set the minimum complexity to some large number and then choose the desired enzymes from the picker. Checking a highlighted enzyme will change its color in the map. All enzyme names in the Enzyme Picker are hyperlinked to explanation windows. ![]() ![]() Enzymes added to the map by default (as specified by the Site Complexity field) are highlighted in the Enzyme Picker. The names of the enzymes specified here will be given a distinct color (and/or appearance), as specified by the Selected Enzymes field. Cleavage site resistance information is based on the enzyme providers' descriptions.Įnzyme Choices Identifies enzymes that will be added to the map, overriding other controls. coli dcm or dam methylation will not be included in the map or fragment list. Reject coli methyl: If set to Yes, restriction sites that are predicted not to be cleaved because of overlapping E. For example, if set to 6, enzymes that recognize unambiguous sequences less than 6 basepairs long, or that recognize a 6 basepair sequence with at least one ambiguous basepair, will not be included in the map. Enter the minimum number of basepairs in the enzyme recognition sequence, adjusted for ambiguity. Site Complexity: Used to reject enzymes that cut too frequently. ![]()
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