Pathway Tools Workshop: Regulation
Enter new transcription unit
You found that HP0167 and HP0168 form a transcription unit; the transcript is ~ 1kb.
Search genes for HP0168.
Add the TU: Gene > New Operon
Enter genes in transcription order: HP0168 HP0167
Add evidence code from drop-down menu (recommended).
You mapped the transcription start site by primer extension to 27 bp upstream of the HP0168
ORF. You do not know which sigma factor is used.
Enter “-27” in the “distance from fist gene” box. After you click outside the box, the sequence
surrounding the tss (in capital letter) will be shown, allowing you to double-check the location.
Add evidence code from drop-down menu.
If known sigma factors have been classified under the |Sigma-Factors| class in your PGDB, and you
know the sigma factor used at this promoter, you can select it from a list of known sigma factors. Some
classification of sigma factors is now done by Pathologic (based on the protein name);
additions/corrections must be made via the ontology editor.
Add a regulatory interaction
You found that HP0176 is overexpressed in a tenA mutant; thus, the transcription factor TenA
seems to repress expression of the HP0168-0167 TU. Footprinting experiments have defined the
TenA binding site; it covers 17 bp and its center is located 97 bp upstream of the
transcription start site.
Right-click on TU > Edit > Create Regulatory Interaction
Enter “TenA” into the “Protein” box for the binding site. Select “Repressor” from the “Function” menu.
Editing transcription units: add terminators
Right-click on TU name > Edit > Edit Terminators
Classify sigma factors under the appropriate class Sigma-Factors
Go to the gene/protein page for the sigma factor, e.g HP0088-MONOMER.
Right-click the name > Edit > Protein Editor
Click on the “Class” button and select “a sigma factor” in addition to “a polypeptide” (i.e. do not
unselect “a polypeptide”).