Input sequence : format

Please input the nucleotide sequence only, or use the Fasta format.
Examples:

Binding factor

The binding factor refers to the transcription factor regulating the gene.

Regulated gene

The first gene in the operon regulated by the transcription factor.

Sigma factor

The sigma factor transcribing the gene, if known.

Regulation

This column describes how the transcription factor regulates the gene. Options are positive, negative, both, promoter (in case of a sigma factor), and unknown


Absolute position

We recalculated the absolute position of each cis-element using the NCBI sequence file (accession number NC_000964).
ND : No Data.

Location

Location of the binding site with respect to the transcription start site.

Binding sequence (cis-element)

We show the cis-element as well as nearby sequences.
Red characters correspond to the exact binding sequence, as shown in the reference.
Bold face shows the transcription start site.

Abbreviations of Experimental Techniques Used

Abbrev.Description
AR DNA microarray and macroarray
DB Disruption of Binding Factor gene
DP Deletion assay
FT Footprinting assay (DNase I, DMS, etc.)
GS Gel retardation assay
HB Slot blot analysis
HM Homology search
OV Overexpression of Binding Factor gene
PE Primer extension analysis
RG Reporter gene (e.g., lacZ assay)
RO Run-off transcription assay
ROMA Run-off transcription followed by macroarray analysis
S1 S1 mapping analysis (S1 nuclease transcript mapping)
SDM Site-directed mutagenesis (Oligonucleotide-directed mutagenesis)
NDNo Data

Marks

mark meaning
red No orthologous gene found.
red Orthologous gene present.
red Orthologous gene present, as well as a cis-element like sequence in the promoter region.

phylum color No. of species
Actinobacteria orange 4
Chlamydiae yellow 2
Cyanobacteria green 2
Firmicutes red
12
Proteobacteria blue 24
Spirochaetes purple 2
others gray 4
TOTAL
50

Go to Taxonomy


Phylogenetic profile

PHYLOGENETIC CONSERVATION STUDY
We've tried to display the results of an analysis into a systematic survey of the conservation of known cis-elements, as well as their binding factors, through available eubacterial genome sequences. To do this, we used the orthology information of the COG database and applied the above-mentioned weight matrices/consensus patterns to the upstream sequence of orthologous genes.



Weight Matrix Search (by weight matrix)

This program returns the top 10 similar weight matrices against your input weight matrix.

Use a tab (or space) deliminated format.
The first line, if starting with ">", is ignored.
Both absolute numbers and relative frequencies are acceptable.
Input nucleotides should be in the order A->C->G->T.

Example:
Nucleotide Position
A0 0 7 7 7 7 1 6 7 2 0 0 0 0 1
C0 7 0 0 0 0 0 1 0 0 0 1 0 0 6
G7 0 0 0 0 0 2 0 0 0 0 0 0 7 0
T0 0 0 0 0 0 4 0 0 5 7 6 7 0 0

Example format 1:
>RocR
0 0 7 7 7 7 1 6 7 2 0 0 0 0 1
0 7 0 0 0 0 0 1 0 0 0 1 0 0 6
7 0 0 0 0 0 2 0 0 0 0 0 0 7 0
0 0 0 0 0 0 4 0 0 5 7 6 7 0 0

Example format 2:
0 0 1 1 1 1 0.143 0.857 1 0.286 0 0 0 0 0.143
0 1 0 0 0 0 0 0.143 0 0 0 0.143 0 0 0.857
1 0 0 0 0 0 0.286 0 0 0 0 0 0 1 0
0 0 0 0 0 0 0.571 0 0 0.714 1 0.857 1 0 0