Skip to content

Commit

Permalink
nrps_pks_modules: change text to be clearer
Browse files Browse the repository at this point in the history
  • Loading branch information
SJShaw committed Dec 11, 2024
1 parent 307ff08 commit 7f6c5c1
Showing 1 changed file with 4 additions and 4 deletions.
8 changes: 4 additions & 4 deletions docs/modules/nrps_pks_modules.md
Original file line number Diff line number Diff line change
Expand Up @@ -47,10 +47,10 @@ In the examples above, the adenylation domain (`A`) is predicted to load leucine

![module-types](../img/modules_types.png)

Not all modules will be considered *complete* like `orf_R7` in the image above.
Along with *complete* modules, e.g. in `orf_R7` above, some *incomplete* modules are annotated (e.g. `orf_R6`)
It is common to have large fragments of domains and multiple domains that by themselves don't complete a module.
In cases where these domains are found and cannot form a *complete* module, an *incomplete* module will be formed.
Incomplete modules are shown with a dashed outline and will always show component domains, an example is `orf_R6` in the image above.
Incomplete modules are shown with a dashed outline and will always show component domains.
In the case of a loader domain without a carrier protein, the predicted substrate that would be loaded is not considered for a candidate cluster's polymer prediction.

There are also occasions, even in a complete module, where no consensus can be found for the prediction of a loaded substrate.
Expand Down Expand Up @@ -82,8 +82,8 @@ In this visualistion, the gene ordering is as predicted for that particular cand

Gene arrows, which can be clicked to highlight that gene in the cluster viewer, indicate the extent of genes.

Modules are number, e.g. `M 5`, and shown with lines that indicate the extent of the module.
Modules are numbered, e.g. `M 5`, and shown with lines that indicate the extent of the module.
In the example above, module 7 is a cross-gene module, with the module line crossing the boundaries of `kirAIII` and the gene to the right.
Below the module number is the predicted monomer of the module.

A legend is included in the visualisation to explain the various notations, one example of which is the inactive KR domain in module 8.
A legend is included in the visualisation to explain the various notations, one example of which is the inactive `KR` domain in module 8.

0 comments on commit 7f6c5c1

Please sign in to comment.