Short Manual for the ProPr54 Web Server

Input


Option 1: Predict Sigma54 promoters and regulon in a genome

This is the most comprehensive option of ProPr54 to predict the Sigma54 regulon in bacterial genomes. The predicted regulon is based on the sigma54 promoters in intergenic regions and proteins with similarity to known sigma54 regulons.
  • Full genome: Fasta file of a complete genome (.FNA) and the associated annotation file (.GFF)
  • WGS: Fasta file with all contigs of the Whole Genome Sequence (WGS) (.FNA) and the associated annotation file (.GFF)
  • Large DNA Fragments: Fasta file with all large DNA fragments (.FNA) and the associated annotation file (.GFF)

Option 2: Predict Sigma54 promoters in a list of short sequences

This option will screen short sequence of typicaly 60-300 nt only for the presence of Sigma54 promoters. No annotation file is used.
  • List of short sequences: A Fasta file of all fragments to be screened (.FNA) or (.fasta).

Additional option: Annotation of genomes

If an annotation file (.GFF) is not available this can be created within a minute by our FACoP web server
  • Full genome or WGS: Submit the fasta file (.FNA) to our server:


RESULTS


WebLogo

On the basis of all predicted Sigma54 binding sites a graphical representation of the binding motif is made as a WebLogo: https://weblogo.threeplusone.com/

Sigma54 Motifs

All predicted motifs including its start and end postition of the Sigma54 binding site are listed in this table. The kmer columns shows the up and downstream sequence of the predicted sigma54 motif. The locus-tag represent the first gene downstream of the predicted motif

Regulon Genes

All proteins encoded by the genome are screened for similarity (Blastp) to known Sigma54 regulon proteins in the UniProt database. The Blast scores are given in this table. For more info on blast values see https://blast.ncbi.nlm.nih.gov/doc/blast-help/

Intersection

The first gene downstream of a sigma54 promoter which also show similarity to known sigma54 regulon members are listed here.

Combined

All genes downstream of a sigma54 promoter and genes which show similarity to known sigma54 regulon members are listed here. Also the distance between the motif and the start of the gene is reported in this table.

Downloads

To allow the user in-depth analysis a functional annotation is done. Especially, the operon prediction might be great value. This enables to make any combinated need to further study on the predicted regulon. For aligning table we advice to use VLOOKUP in excel or use our online 'Align Tables' tool of Genome2D web server

Bookmark results

Bookmark your session here for later use. Results are stored for 60 days on the server.

Start new Session

Once you saved your bookmark you can initialize a new session here.

Anne de Jong and Tristan Achterberg