RegulonDB RegulonDB 10.9: Sigmulon form help
Sigmulon form help

Outline and description of the labels for the Sigmulon page.

Sigma Factor
Name: Name of the sigma factor.
Synonym(s): Alternative names that identify the same sigma factor.
Gene name(s): Name of gene producing the sigma factor.
Coregulator(s): Transcription factors regulating promoters expressed by the sigma factor.
Notes: Transcription factors regulating promoters expressed by the sigma factor.
Sigmulon Genes: Names of the genes transcribed by the sigma factor.
Transcribed Promoters
Promoter name: Names of the promoters transcribed.
TSS Position: Transcription start site (+1) corresponds to the first nucleotide transcribed during transcription initiation.
Transcribed genes: Names of the transcribed genes.
TSS distance: Distance from the transcription starting site (+1) to beginning of the gene (signal initiation of translation, commonly ATG).
Promoter Sequence:

DNA sequence that enables a gene to be transcribed. The nucleotide sequence shown spans 60 base pairs upstream and 20 downstream from TSS position +1 (upper-case red nucleotide). The -10 or -12 and -35 or -24 regions are also highlighted in boxes, when they are known.

Method used to obtain -10 and -35 weight matrices.

We use, WCONSENSUS, a program that extracts and aligns motifs within a given input of unordered sequences producing a representative frequency matrix from the alignment, to generate multiple alignments and weight matrices for each set of Transcription Start Sites of each sigma factor.
The strategy is shown in Figure 2 in [Huerta & Collado-Vides, JMB, 2003]. Briefly, i) For each sigma factor, the promoter regions are aligned with respect to the transcription start site (+1). The first 18 bp upstream of the +1's are used as input to Wconsensus to identify the motifs corresponding to the -10 conserved region. ii) To identify the -35 box, we carry out a re-aligment of the promoter regions anchoring the -10 boxes identified by the program. New sequences of various lengths initiating at 13 bp upstream of the -10 box are used as input to Wconsensus to get the motifs corresponding to the -35 conserved region.

box(-10,-12): DNA sequence essential for recognition of the promoter by a sigma factor. This sequence is commonly called -10 or -12, because the sigma factor (70 or 54, respectively) binds to the promoter in roughly 10 or 12 base pairs upstream from the TSS (+1).
box(-35,-24): DNA sequence essential for recognition of the promoter by a sigma factor. This sequence is commonly called -35 or -24, because the sigma factor (70 or 54, respectively) binds to the promoter in roughly 35 or 24 base pairs upstream from the TSS (+1).
Evidence Code: System used to abbreviate with letters according to meanings of the experimental or computational methods that support some information about a transcription process.
Reference(s): Original literature source where some information about a regulatory interaction was obtained.
Evidence
Evidence: Definition of experimental or computational methods that support some information about a transcription process.

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