@drew.b.ferrell has already demonstrated one way of doing this. If all of your sequences are from "RefSeq Protein" then you could download "refseq_protein" blast database indexes from NCBI via this page. Use the method above from drew.b.ferrell to get accession numbers.

Then you can use blastdbcmd utility from blast+ package to retrieve sequences you need (sequence truncated).

$ blastdbcmd -db refseq_protein -entry WP_051684486.1 -outfmt %f
>WP_051684486.1 ATP-binding cassette domain-containing protein [[Clostridium] aminophilum]
MSIFGEQFLARRNRDQIDLDNALQDVYEAVTGRESIRYSINSDEQVRKELERICFYLGVRADQDVPEYNDLEDMLDYITR
PFAIMRRHILLTHHWWKNGDGPLLVSKKDSDELLALIPGRLGGYYYTDFRSNKKIKLDRHNAGEFEKEAICFYKPLPLSS
LSANELTGLLFKNMAAADLAMLVLSGIGIVGVSLLIPFATKMVFEYVIPTGAMTLVGSFSFLLISSAMVAYIIAVIKQGY

You can put all of your accession numbers in a file and then feed that in to blastdbcmd (-entry_batch option). Doing this locally will be much faster than Entrezdirect but will require you to download the refseq_protein blast database index.

Right, so there may be some manual work. If you have access to a Unix machine, how many entries do you get with

grep '>' my_fasta.fa | sed 's#\.[[:digit:]].*##' | uniq

edit: I was able to use the Eutils command-line tools from NCBI (https://www.ncbi.nlm.nih.gov/books/NBK179288/). But you need all your protein IDs in a sequence separated by a comma, which we can do.

Just get the installer, run the shell file to install, and move into that directory.

./install-edirect.sh \
cd edirect

Then we need your protein sequence IDs.

Here's my fasta:

cat tmp.fa
>WP_051684486.1
MSIFGEQFLARRNRDQIDLDNALQDVYEAVTGRESIRYSINSDEQVRKELERICFYLGVRADQDVPEYND
LEDMLDYITRPFAIMRRHILLTHHWWKNGDGPLLVSKKDSDELLALIPGRLGGYYYTDFRSNKKIKLDRH
NAGEFEKEAICFYKPLPLSSLSANELTGLLFKNMAAADLAMLVLSGIGIVGVSLLIPFATKMVFEYVIPT
GAMTLVGSFSFLLISSAMVAYIIAVIKQGYADRVKVRMEVYLTHGVMGRMINFPTSFFASKSTGELYRVF
DNLREIPQILIDSVIVPIIDISLAMLFIIQIAVIVPELLVPAVITVLLQFVCMAIGTFQAYGLLNIELQQ
DRKIQGLAISVYEGIQRIKLSGSESRIMAKWAGLYSKKAKVAYPAVFPVRFQTEMIAFISMMGMLAAFYK
GFTDNISISQFVAFVAAFGMLTGSITAFSNKSKDVIKLKPVLKMSDEILKECPEVSKEKLIVDHLSGKIE
VKDLTFRYGRDLPLILDGVSFTVHPGEYVAIVGKSGCGKSTLVRIFMGFEKAVSGSVSYDDIDVERIDPR
SLRRSIGVVMQSGNLFYDSIYRNIAISAPGLSMEEAWEAAEKAGIAEDIRNMPMKMKTLIPQGGGGISGG
QRQRIMIARALAAKPNILIFDEATSALDNITQKVVQDSLDQLNCTRIVIAHRLSTIQNCDRILVLDKGRI
IEEGNYQELLKKGGFFANLIKRQQL
>WP_013276004.1
MEVLKVSAKSNPNAVAGALAGVIREKGGAEIQIIGAGALNQAVKAIAIARGYVAPSGIDLICIPAFTDIE
IDGQQRTAIKLIVEPR

We can get the protein seq ids comma-separated.

grep '>' tmp.fa | sed 's#>##' | tr  '\n' ',' | sed 's#,$##' > protein_ids.csv

cat protein_ids.csv
WP_051684486.1,WP_013276004.1

Here you have a few options, but I guess one option is to just copy that string into the next command:

esearch -db protein -query WP_051684486.1,WP_013276004.1 | efetch -format fasta
>WP_051684486.1 ATP-binding cassette domain-containing protein [[Clostridium] aminophilum]
MSIFGEQFLARRNRDQIDLDNALQDVYEAVTGRESIRYSINSDEQVRKELERICFYLGVRADQDVPEYND
LEDMLDYITRPFAIMRRHILLTHHWWKNGDGPLLVSKKDSDELLALIPGRLGGYYYTDFRSNKKIKLDRH
NAGEFEKEAICFYKPLPLSSLSANELTGLLFKNMAAADLAMLVLSGIGIVGVSLLIPFATKMVFEYVIPT
GAMTLVGSFSFLLISSAMVAYIIAVIKQGYADRVKVRMEVYLTHGVMGRMINFPTSFFASKSTGELYRVF
DNLREIPQILIDSVIVPIIDISLAMLFIIQIAVIVPELLVPAVITVLLQFVCMAIGTFQAYGLLNIELQQ
DRKIQGLAISVYEGIQRIKLSGSESRIMAKWAGLYSKKAKVAYPAVFPVRFQTEMIAFISMMGMLAAFYK
GFTDNISISQFVAFVAAFGMLTGSITAFSNKSKDVIKLKPVLKMSDEILKECPEVSKEKLIVDHLSGKIE
VKDLTFRYGRDLPLILDGVSFTVHPGEYVAIVGKSGCGKSTLVRIFMGFEKAVSGSVSYDDIDVERIDPR
SLRRSIGVVMQSGNLFYDSIYRNIAISAPGLSMEEAWEAAEKAGIAEDIRNMPMKMKTLIPQGGGGISGG
QRQRIMIARALAAKPNILIFDEATSALDNITQKVVQDSLDQLNCTRIVIAHRLSTIQNCDRILVLDKGRI
IEEGNYQELLKKGGFFANLIKRQQL
>WP_013276004.1 MULTISPECIES: stage V sporulation protein S [Thermosediminibacter]
MEVLKVSAKSNPNAVAGALAGVIREKGGAEIQIIGAGALNQAVKAIAIARGYVAPSGIDLICIPAFTDIE
IDGQQRTAIKLIVEPR