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The C-terminal portion of the receptor includes the ligand binding domain which recognizes specific hormones, vitamins, retinoids or other lipophilic compounds.
Transcription factors can be made up of multiple protein domains, and these might include a DNA binding domain (which recognizes specific target DNA sequences) or a domain that interacts with the transcriptional machinery to regulate the expression of genes.
In contrast, the phage endolysins generally contain an enzymatically active domain and a cell-wall binding domain which recognizes highly-specific ligands on the host cell surface [ 27], and thus each domain is under strong directional selective pressures.
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The transposase has an N-terminal DNA-binding domain, which recognizes the IR in a sequence-specific manner, and a C-terminal catalytic domain.
In flowering plants, ARF proteins possess a conserved DNA-binding domain which recognizes auxin responsive elements (AuxREs): short motifs which are found in the promoter sequences of many auxin-responsive genes [ 7, 8].
The closest nucleic acid-binding relative of the Prp3 ssRNA-binding domain is the IS608 transposase domain, which recognizes DNA.
In several bacteria the PrsW domain is fused to intracellular signaling domains such as the PilZ domain which recognizes cyclic diguanylate, cyclic nucleotide binding domains, phosphopeptide-binding FHA domains and Zn-ribbon domains [ 65] (Additional file 1).
The immunophilin FKBP52 is composed of three domains, an FK506-binding domain with peptidyl-prolyl isomerase activity, an FKBP-like domain of unknown function and a TPR-clamp domain, which recognizes the C-terminal peptide of Hsp90 with high affinity.
The co-localization required the UBA domain, which recognizes pUb.
HrpX contains AraC-type of DNA binding domain, which specifically recognizes the plant-inducible promoter (PIP) box (TTCGC-N15-TTCGC) and imperfect PIP box (TTCGC-N8-TTCGT) present in the cis-regulatory regions of hrp gene cluster [ 36- 38].
The second class of proteins likely involved in the dominant negative interaction are the PDZ binding domain family of proteins that have the class 1 PDZ domains which recognizes the QDTRL sequence in the end of the CFTR C terminus.
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