Pyridoxal 5’-phosphate synthesis and salvage in Bacteria and Archaea: predicting pathway variant distributions and holes

Supplementary data for ‘Pyridoxal 5’-phosphate synthesis and salvage in Bacteria and Archaea: predicting pathway variant distributions and holes’ as published in Microbial Genomics.

## Supplemental data 1

This folder contains images of the sequence similarity network (SSN) evolution, the different proteins annotated as part of the PLP de novo synthesis or salvage pathway, and relative proteins. These proteins were detected using the 113 temporary HMM profiles created at the end of Step1 of the method and used at the beginning of Step2 (see SupMat or Figure2).

Each folder contains the representation of the SSN of each family of proteins with the evolution of the alignment threshold. The number of each image represents the alignment score used as a threshold (meaning that all the edges represent an alignment score >= X, with X the alignment threshold).

In each family folder, the protein (the node inside the SSN) is colored based on the annotation made by KofamKOALA or eggNOG-Mapper v2, depending on the folder's name.

In case there is a Step_1 and Step_2 in the folder, a deeper analysis was done to have a more stringent alignment threshold for some clusters identified using the alignment threshold of the Step_1. This was done because some proteins are more related than others in the same family and a unique alignment threshold is not suitable to separate all the proteins inside a family. For example, epd, gapB and gapA are more connections between each other than epd and asd or argC.

You can also find in the folder of each family the SSN network in XML format and a tsv file containing the attribution of the protein to a cluster after selecting the appropriate alignment threshold.