scholarly journals PredictRegulon: a web server for the prediction of the regulatory protein binding sites and operons in prokaryote genomes

2004 ◽  
Vol 32 (Web Server) ◽  
pp. W318-W320 ◽  
Author(s):  
S. Yellaboina ◽  
J. Seshadri ◽  
M. S. Kumar ◽  
A. Ranjan
Keyword(s):  
Protein Binding ◽  
Binding Sites ◽  
Regulatory Protein ◽  
Web Server ◽  
Protein Binding Sites

scholarly journals GenProBiS: web server for mapping of sequence variants to protein binding sites

2017 ◽  
Vol 45 (W1) ◽  
pp. W253-W259 ◽  
Author(s):  
Janez Konc ◽  
Blaz Skrlj ◽  
Nika Erzen ◽  
Tanja Kunej ◽  
Dusanka Janezic
Keyword(s):  
Protein Binding ◽  
Binding Sites ◽  
Web Server ◽  
Sequence Variants ◽  
Protein Binding Sites

Functional analysis of eve stripe 2 enhancer evolution in Drosophila: rules governing conservation and change

Development ◽  
1998 ◽  
Vol 125 (5) ◽  
pp. 949-958 ◽  
Author(s):  
M.Z. Ludwig ◽  
N.H. Patel ◽  
M. Kreitman
Keyword(s):  
Protein Binding ◽  
Reporter Gene ◽  
Dna Sequences ◽  
Binding Sites ◽  
Regulatory Protein ◽  
P Element ◽  
Systematic Change ◽  
Stabilizing Selection ◽  
Protein Binding Sites ◽  
Adaptive Mutations

Experimental investigations of eukaryotic enhancers suggest that multiple binding sites and trans-acting regulatory factors are often required for wild-type enhancer function. Genetic analysis of the stripe 2 enhancer of even-skipped (eve), an important developmental gene in Drosophila, provides support for this view. Given the importance of even-skipped expression in early Drosophila development, it might be predicted that many structural features of the stripe 2 enhancer will be evolutionarily conserved, including the DNA sequences of protein binding sites and the spacing between them. To test this hypothesis, we compared sequences of the stripe 2 enhancer between four species of Drosophila: D. melanogaster, D. yakuba, D. erecta and D. pseudoobscura. Our analysis revealed a large number of nucleotide substitutions in regulatory protein binding sites for bicoid, hunchback, Kruppel and giant, as well as a systematic change in the size of the enhancer. Some of the binding sites in D. melanogaster are either absent or modified in other species. One functionally important bicoid-binding site in D. melanogaster appears to be recently evolved. We, therefore, investigated possible functional consequences of sequence differences among these stripe 2 enhancers by P-element-mediated transformation. This analysis revealed that the eve stripe 2 enhancer from each of the four species drove reporter gene expression at the identical time and location in D. melanogaster embryos. Double staining of native eve protein and transgene mRNA in early embryos showed that the reporter gene mimicked native eve expression and, in every case, produced sharply defined stripes at the blastoderm stage that were coincident with eve stripe 2 protein. We argue that stripe 2 eve expression in Drosophila evolution can be viewed as being under constant stabilizing selection with respect to the location of the anterior and posterior borders of the stripe. We further hypothesize that the stripe 2 enhancer is functionally robust, so that its evolution may be governed by the fixation of both slightly deleterious and adaptive mutations in regulatory protein binding sites as well as in the spacing between binding sites. This view allows for a slow but continual turnover of functionally important changes in the stripe 2 enhancer.

scholarly journals PBSword: a web server for searching similar protein-protein binding sites

2012 ◽  
Vol 40 (W1) ◽  
pp. W428-W434 ◽  
Author(s):  
B. Pang ◽  
X. Kuang ◽  
N. Zhao ◽  
D. Korkin ◽  
C.-R. Shyu
Keyword(s):  
Protein Binding ◽  
Binding Sites ◽  
Web Server ◽  
Protein Binding Sites ◽  
Similar Protein
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