Bacterial Promoter Spacing
Check the inter-box gap between supplied bacterial minus-35 and minus-10 promoter motifs.
Description
Bacterial promoter boxes have a gap between their sequence boundaries.
Bacterial promoter boxes have a gap between their sequence boundaries. The gap differs from the distance between box starts.
Check the inter-box gap between supplied bacterial minus-35 and minus-10 promoter motifs.
When to use Bacterial Promoter Spacing
Use this for the following task: Check the inter-box gap between supplied bacterial minus-35 and minus-10 promoter motifs.
Prepare the observed records or explicit model parameters requested below. Keep probabilities as fractions and paired records aligned.
How to use Bacterial Promoter Spacing and understand its results
- Prepare the observed records or explicit model parameters requested below. Keep probabilities as fractions and paired records aligned.
- Enter minus35Start, minus35Length, minus10Start, minimumGap, maximumGap using the field table, then run the tool.
- Read interBoxGapBp, withinSpacing. Interpret flags, units, ordering and placeholder values using the rules below.
- Review any reported issue or failed check, correct the supplied values when appropriate, and verify the result in its intended context.
| Input field | Meaning | Value type and bounds | Requirement |
|---|---|---|---|
| minus35Start | Minus 35 start | number | Required |
| minus35Length | Minus 35 length | integer | Required |
| minus10Start | Minus 10 start | number | Required |
| minimumGap | Minimum gap | number | Required |
| maximumGap | Maximum gap | number | Required |
Use nonnegative start coordinates, positive minus-35 length and ordered nonnegative gap bounds. Require nonoverlapping ordered boxes and compare the gap inclusively.1
gap = minus10Start−minus35Start−minus35Length This summarizes the declared operation. Units, indexing, inclusivity and exceptional cases are explained in the surrounding text.
| Output field | Meaning | Value type |
|---|---|---|
| interBoxGapBp | Inter box gap bp | number |
| withinSpacing | Within spacing | boolean |
{
"input": {
"minus35Start": 0,
"minus35Length": 6,
"minus10Start": 23,
"minimumGap": 16,
"maximumGap": 18
},
"output": {
"interBoxGapBp": 17,
"withinSpacing": true
}
}Limitations and assumptions
Motifs and their locations are inputs. This does not detect promoter sequences or predict transcription strength.
The tool evaluates supplied observations or a declared model. It does not establish the biological cause of an observed pattern. Malformed requests produce input errors. A successfully evaluated request can still contain false flags, empty result lists or a result outside the supplied threshold; those outcomes have the meanings stated above.
Alternative or Complementary methods
Choose Ribosome Binding Spacing for this operation: Locate AGGAGG ribosome-binding motifs at compatible spacing before a specified ATG start. For a complementary task, use Operon Coding Interval Audit for this operation: Audit coding intervals in one bacterial transcript and count its cistrons.
The implementation reference documents the exact calculation, supported input shapes and returned fields.
References
-
Bacterial Promoter Spacing — tool.io
Similar or alternative tools
- Ribosome Binding Spacing
Locate AGGAGG ribosome-binding motifs at compatible spacing before a specified ATG start.
- Operon Coding Interval Audit
Audit coding intervals in one bacterial transcript and count its cistrons.