Perhaps the following link will help:

https://www.biostars.org/p/103891/

There is a link to a multiple sequence alignment tool on NCBIs BLAST page

http://www.ncbi.nlm.nih.gov/tools/cobalt/cobalt.cgi?LINK_LOC=BlastHomeLink

You can input a list of accession No.s or a multifasta file containing all the hits and query sequence.

I haven't used either, if I was in your situation my self I would extract the hits from the proteome database using the blastdbcmd tools (local blast installation) and align the sequences with a different alignment tool.

Here is my script for generating multiple sequences alignment from blast result in tabular format (blast2 with "-m 8" option). I wrote it for DNA alignment but you can use it for AA sequences alignment also.

https://github.com/TnSrk/BioinformaticsScripts/blob/master/hitclust.py

This script should run on UBUNTU OS with blast2 package (Old BLAST version) and MUSCLE  or CLUSTALW or MAFFT

USAGE 

1. create QeuryDataBase with fastacmd 

   eg. "formatdb -o T Query.faa"

2. create SubjectDataBase with fastacmd

   eg. "formatdb -o T Subject.faa"

3. run "blast2" with -m 8 option 

  eg. "blastall -p blastp -d Subject.faa -i Query.faa -m 8 > Result.blast.tab"

4. run this command

python hitclust.py -a 2 --grouping=1 --minmatchlen=30 -n 1 -t "QeuryDataBase_Path" -r "SubjectDatabase_Path" -i Tabular_BLAST_Result > OUTPUT

Alignment will kept in OUTPUT file

Please feel free to contact me If you have any questions or suggestions.

Thanks Tanawut Srisuk.  The other issue with this, is getting good and useful names for each sequence in the alignment, and the Sequence Name Annotation-based Designer tool works well for that:  http://veb.lumc.nl/SNAD/convert.cgi?item=Execution#output

 Hello i would like some help with multi-alignment using CLutalW, t-coffee or NCBI Blast. How am I to use the source commands you have provided Tanawut Srisuk?

You might want to try MVIEW as well (https://desmid.github.io/mview)

Joseph D Tingling. In order to use other alignment program you can modify the script's option from "-a 2" to "-a 0" for MUSCLE or "-a 1" for mafft and those programs must be installed in the system, my script just call them via python subprocess module. For t-coffee I did not included it yet. If you need to use tho program please let me know. I'll find the time to test and included it to the script. 

ps. Sorry for my late reply. I just see your comment.

@ Bruno Contreras-Moreira 

Thank you for MVIEW info !!! It is marvelous !!!