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Not exactly clear what you are asking.

If you are blasting UniProt, e.g. https://www.uniprot.org/blast/ , you can set an E-Threshold. The lower the threshold is, the higher the similarity has to be for a hit to show up in the results - a threshold setting appropriate to your requirement can greatly reduce the number of "unwanted" results. You can also specify how many hits you want to maximally get: if you lower that number from the default 250 to 50, you only get the 50 best hits.Once you have run your search, you get an overview of the hits you find, and based on this, you can select which ones you want to include in the alignment and/or download. If you are not getting anything in the download, you probably failed to check any of the sequences in the results list for download (checkboxes to the left of the individual entries). If you want to download the sequences, you have to download them as a FastA file, this gives you the raw, unaligned sequences. You can then use a local program, e.g Clustal http://www.clustal.org/clustal2/ to generate the alignment.

If you want to do the alignment on the Uniprot website, first click the "align" tab. Once the job has finished , you can download the alignment as text file, as a fastA file or as a jalview file (http://www.jalview.org/getdown/release/ , an alignment viewer). I generally go for the fastA format, as this is a plain text format compatible with further processing with local programs.

If you use other sites to do your search, the details of the interface will differ, but the type of parameters you can adjust to narrow down the results to just the level of similarity you want will be similar.

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Dear Annemarie

You exactly answered my question. I will try it. Thanks for your invaluable help.