In your experiment focused on studying ubiquitin transfer using confocal microscopy, it's crucial to choose a fluorescent tag that not only provides reliable visualization but also minimally interferes with the protein's activity. Considering your concern about the size of the GFP tag potentially affecting protein function, here are some alternative small-sized fluorescent tags that you can consider for studying in vivo protein activity:

1. mCherry Tag: The mCherry fluorescent protein is relatively small and has been successfully used in various live-cell imaging studies. Its compact size may help reduce interference with protein activity compared to larger tags.

2. HaloTag: HaloTag is a small protein tag that forms a covalent bond with ligands, allowing for specific and reversible labeling. This tag has been utilized for in vivo protein imaging and tracking.

3. SNAP-Tag: Similar to HaloTag, the SNAP-tag system enables specific and covalent labeling of proteins. Its small size makes it a suitable candidate for minimizing interference with protein function.

4.TurboGFP: TurboGFP is a brighter and more stable variant of GFP. While still larger than some of the other small tags, it offers enhanced fluorescence properties and has been successfully used for protein labeling.

5. mEOS: mEOS is a photoconvertible fluorescent protein that changes color from green to red upon exposure to UV light. This property can help distinguish between newly synthesized and pre-existing protein pools.

6. sfGFP: Superfolder GFP (sfGFP) is a compact GFP variant that folds efficiently even when fused to other proteins. It's small size and robust folding characteristics make it a potentially suitable tag for your in vivo studies.

7. Dendra2: Dendra2 is another photoconvertible fluorescent protein that shifts from green to red fluorescence upon exposure to UV or blue light. This can be useful for tracking protein dynamics over time.

8. Blue Fluorescent Proteins (BFPs): BFPs, such as TagBFP, are smaller than GFP and provide a distinct color for multicolor imaging experiments.

Before finalizing your choice of fluorescent tag, it's recommended to perform pilot experiments to confirm that the tag does not significantly affect the ubiquitin protein's activity and behavior. This can include assessing protein localization, interactions, and function in the presence of the tag.

Alternatively, if you're open to alternative methods, you could consider using techniques like proximity ligation assays (PLA) or Förster resonance energy transfer (FRET) to study protein-protein interactions and ubiquitin transfer without the need for direct fluorescent labeling. These methods can provide valuable insights into protein dynamics while minimizing the impact on protein activity.