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Protein tags are peptide sequences genetically grafted onto a recombinant protein. Often these tags are removable by chemical agents or by enzymatic means, such as proteolysis or intein splicing. Tags are attached to proteins for various purposes. They can be added to either end of the target protein, so they are either C-terminus or N-terminus specific or are both C-terminus and N-terminus specific. Some tags are also inserted into the coding sequence of the protein of interest; they are known as internal tags.
Solubilization tags are used, especially for recombinant proteins expressed in chaperone-deficient species such as E. coli, to assist in the proper folding in proteins and keep them from precipitating. These include thioredoxin (TRX) and poly(NANP). Some affinity tags have a dual role as a solubilization agent, such as MBP, and GST.
Chromatography tags are used to alter chromatographic properties of the protein to afford different resolution across a particular separation technique. Often, these consist of polyanionic amino acids, such as FLAG-tag.
Fluorescence tags are used to give visual readout on a protein. GFP and its variants are the most commonly used fluorescence tags. More advanced applications of GFP include using it as a folding reporter (fluorescent if folded, colorless if not).
Protein tags may allow specific enzymatic modification (such as biotinylation by biotin ligase) or chemical modification (such as reaction with FlAsH-EDT2 for fluorescence imaging). Often tags are combined, in order to connect proteins to multiple other components. However, with the addition of each tag comes the risk that the native function of the protein may be abolished or compromised by interactions with the tag. Therefore, after purification, tags are sometimes removed by specific proteolysis (e.g. by TEV protease, Thrombin, Factor Xa or Enteropeptidase).
His-tag, 5-10 histidines bound by a nickel or cobalt chelate (HHHHHH)
Myc-tag, a peptide derived from c-myc recognized by an antibody (EQKLISEEDL)
NE-tag, an 18-amino-acid synthetic peptide (TKENPRSNQEESYDDNES) recognized by a monoclonal IgG1 antibody, which is useful in a wide spectrum of applications including Western blotting, ELISA, flow cytometry, immunocytochemistry, immunoprecipitation, and affinity purification of recombinant proteins 
Rho1D4-tag, refers to the last 9 amino acids of the intracellular C-terminus of bovine rhodopsin (TETSQVAPA). It is a very specific tag that can be used for purification of membrane proteins.
S-tag, a peptide derived from Ribonuclease A (KETAAAKFERQHMDS)
SBP-tag, a peptide which binds to streptavidin (MDEKTTGWRGGHVVEGLAGELEQLRARLEHHPQGQREP)
Softag 1, for mammalian expression (SLAELLNAGLGGS)
SnoopTag, a peptide which binds covalently to SnoopCatcher protein (KLGDIEFIKVNK). A second generation, SnoopTagJr, was also developed to bind to either SnoopCatcher or DogTag (mediated by SnoopLigase) (KLGSIEFIKVNK)
DogTag, a peptide which covalently binds to DogCatcher (DIPATYEFTDGKHYITNEPIPPK), and can also covalently bind to SnoopTagJr, mediated by SnoopLigase 
SdyTag, a peptide which binds covalently to SdyCatcher protein (DPIVMIDNDKPIT). SdyTag/SdyCatcher has a kinetic-dependent cross-reactivity with SpyTag/SpyCatcher.
BCCP (Biotin Carboxyl Carrier Protein), a protein domain biotinylated by BirA enabling recognition by streptavidin
^ abSchmidt, Thomas G.M.; Koepke, Jürgen; Frank, Ronald; Skerra, Arne (1996). "Molecular Interaction Between the Strep-tag Affinity Peptide and its Cognate Target, Streptavidin". Journal of Molecular Biology. 255 (5): 753-66. doi:10.1006/jmbi.1996.0061. PMID8636976.
^Einhauer, A.; Jungbauer, A. (2001). "The FLAG(TM) peptide, a versatile fusion tag for the purification of recombinant proteins". Journal of Biochemical and Biophysical Methods. 49 (1-3): 455-65. doi:10.1016/S0165-022X(01)00213-5. PMID11694294.
^Keefe, Anthony D.; Wilson, David S.; Seelig, Burckhard; Szostak, Jack W. (2001). "One-Step Purification of Recombinant Proteins Using a Nanomolar-Affinity Streptavidin-Binding Peptide, the SBP-Tag". Protein Expression and Purification. 23 (3): 440-6. doi:10.1006/prep.2001.1515. PMID11722181.
^Zakeri, Bijan; Howarth, Mark (2010). "Spontaneous Intermolecular Amide Bond Formation between Side Chains for Irreversible Peptide Targeting". Journal of the American Chemical Society. 132 (13): 4526-7. doi:10.1021/ja910795a. PMID20235501.