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The position weight matrix of CTCF's binding motif is composed of thousands of specific sequences, or motif-words.
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The GTP-binding motif is composed of the G1 to G5 sequences and two conserved motifs (CB, consensus box and IAN motif) [ 9].
The Actinobacteria-specific training set for the identification of the Zur-binding motif was composed of the candidate zinc transporter genes znuABC.
The taxon-specific training sets for identification of Zur-binding motifs were composed of the previously identified Zur-binding sites in Firmicutes, α-, β-, and γ-proteobacteria [ 62] and the DNA motif search profiles were constructed using the SignalX program.
These functional motifs are composed of amino-terminal domain, DNA binding domain with two zinc-fingers, and a ligand binding domain (LBD).
The best-studied USP protein MJ0577-ATP froM.M. janashii contains a typical ATP-binding motif, which is composed of the following residues: G-SH-G- 9X -GSV (where the superscripts indicate the position of each residue in the sequence, FiG-SH-G- 9X -GSV
A single EGR1 binding motif is demonstrated at bp -301 of the human CD44 promoter.
The two globular domains of Sirt3 composed of an NAD binding Rossmann fold and a zinc binding motif are similar to other sirtuins (Avalos et al., 2004; Du et al., 2011; Yuan and Marmorstein, 2012; Jiang et al., 2013).
The binding motif was synthesized as previously described [32].
The consensus binding motif was chosen to be TGTTTAC.
Motif 1 is composed of residues 114 116 (RG D) and motif 2 is composed of residues 125 128 (RQD D).
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