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In proteins, a structural unit exhibiting a particular three-dimensional architecture that is found in a variety of proteins and usually is associated with a particular function. (Figure 3-9) ...

Motifs, themes and thematic maps of an integrated Saccharomyces cerevisiae interaction network ...

Motif over-representation analysis with shuffled matrices
To assess the probability of a PWM's predictions being enriched within as many datasets as observed with the zinger PWMs, we shuffled the PFMs of the zingers and fit a distribution to the results.

A small portion of a protein (typically less than 20 amino acids) that is homologous to regions in other proteins that perform a similar function.
See Multipilicity Of Infection.

Motif finder The Motif finder is used to find six base pair stretches (6-mers) that are over-represented within a given set of upstream sequences. It can be used to identify potential cis-regulatory sequences in a set of genes.

A meaningful pattern of nucleotides or amino acids that is shared by two or more molecules.
Multigene Locus ...

Three-dimensional structure of gene product (protein) with known or implied function. eg DNA binding membrane spanning. A ~ is often inferred from a cDNA sequence.
Related Terms:
Protein ...

~s are simple combinations of secondary structure that occur in many different proteins and which carry out a similar function. An example is the helix-loop helix. It consists of two antiparallel helices at about a 60-degree angle to each other connected by a loop.

A common ~ in the secondary structure of proteins, the alpha helix (α-helix) is a right-handed coiled conformation, resembling a spring, in which every backbone N-H group donates a hydrogen bond to the backbone C=O group of the amino acid four residues earlier ( hydrogen bonding).

This article is licensed under the GNU Free Documentation License. It uses material from the Wikipedia article "DNA sequence".

DNA binding ~: Common sites on different proteins which facilitate their binding to DNA. Examples are leucine zipper and zinc finger proteins. Any such protein is called DNA-binding protein.

A protein binding ~ that contain ~7 regions ~40 aa long containing a conserved W & D. Below is a picture of a WD40 region of Human Groucho/Tle1 (1GXR) from L. H. Pearl, S. M. Roe, L. M. Pickles.
top view
side view ...

Leucine zipper: A ~ found in certain proteins in which Leu residues are evenly spaced through an a-helical region, such that they would end up on the same face of the helix. Dimers can form between two such proteins.

Protein sequence analysis at UCL: Our research concerns protein sequence analysis, primarily exploiting the technique of protein `fingerprinting' (which uses conserved ~s to characterise particular folds and functionalities).

TDAG51 protein is rich in PQ(praline-glutamine) ~ at the C terminal. It's reported that protein rich in PQ ~ probably promote the apoptosis of hippocampal and septal cells independently of Fas.

Helix-turn-helix ~s (← links)
Organelles (← links)
Starter trna (← links)
Eukaryote (← links)
Secretory protein (← links)
Archaea (← links)
Archaebacteria (← links)
Messenger rnas (← links)
Organelle (← links)
Chaperone (← links)
Chaperonin (← links) ...

Domains often contain smaller ~s, consisting of a conserved pattern of amino acids, or of combinations of structural elements formed by the folding of nearby amino acid sequences. An example of a ~ is a helix-loop-helix, which binds to DNA.

Very high repetitions (from 1,000 to over 100,000 copies) of a basic ~ or repeat unit (commonly 100 - 300 base pairs) which occur at a few loci on the genome.
Related Terms:
Three-dimensional structure of gene product (protein) with known or implied function.

The basic plant cell shares a similar construction ~ with the typical eukaryote cell, but does not have centrioles, lysosomes, intermediate filaments, cilia, or flagella, as does the animal cell.

Homeobox. A DNA sequence ~ found in the coding region of many regulatory genes; the encoded amino acid structure has a helix-loop-helix structure.
Homeotic (HOX) gene. Any of a group of genes in which mutation results in the replacement of one body structure by another body structure.

A protein structural ~ common in transcription factors. Leucine zipper is formed by two proteins (homodimmer or heterodimmer) and binds to DNA.
Other Resources
PubMed Google ...

helix- A secondary structural ~ of proteins in which a linear sequence of amino acids folds into a right-handed helix stabilized by internal hydrogen bonding between backbone atoms.

Autoregulatory loops: In this type of regulatory ~, a transcription factor binds to regulatory sequences that regulate its own transcription. Such interactions can be positive (amplifying) or negative (squelching).

Double-stranded helix - A common structural ~ of DNA. Two linear strands of single-stranded DNA fold into a helical shape stabilized internally by hydrogen bonds between complementary base pairs.

where the subscripts indicate the number of residues present. The ~ is named for the finger-like loop of amino acids that protrudes from the zinc binding site (known as the "Cys₂/His₂ finger" (pronounced "siss-two-hiss-two").

Sara O. Dionne1, Douglas F. Lake, William J. Grimes and Margaret H. Smith, Identification of HLA-Cw6.02 and -Cw7.01 allele-specific binding ~s by screening synthetic peptide libraries. Immunogenetics 56, 391-399 (2004).

A small portion of a gene or protein that appears in many genes or proteins that are related in structure; the box usually has some specific function, sometimes called a "~", like binding DNA or interacting with specific proteins or other molecules.
brain ...

Miniature Inverted-repeat Transposable Elements (MITEs)
The recent completion of the genome sequence of rice and C. elegans has revealed that their genomes contain thousands of copies of a recurring ~ consisting of ...

In these molecules, the tetrahedral shape of carbon bonded to four other atoms is often a repeating ~.
Biological molecules recognize and interact with one another with a specificity based on molecular shape.

See also: See also: What is the meaning of Protein, Sequence, Trans, Proteins, DNA?

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