>HMPREF9352_0001 rod shape-determining protein MreC [Streptococcus gallolyticus subsp. gallolyticus TX20005]
MSLAFLFRNSGVVSAISSPIRSVVARVDSVVSAPFRFLDSANEEIRDLFNTYSENKELKQ
KVAELEDQSELIDSLKEENEELNSEIGASSSITSQFSATGKVIVRSPVSWYDSLTVKLGK
KNNITKKMLALSGGGLIGTVSDVDSTTSSITLLSNGSDFNIPIKITTSSAEVYGLLESYD
SDKKCFVITNLNSSVDIEEGDSVVTSGLDGDTVANISVGTVSSVKNSSESLERVVYVTST
ADFSDISYVTIVGD
>HMPREF9352_0002 rod shape-determining protein MreD [Streptococcus gallolyticus subsp. gallolyticus TX20005]
MIKVKFYKNKYFLLLLLFLLMLIDGQLSFLASSIFSYHLKVSSHLLLLAVLYFYHDKNKY
FMFISSLVLGGIFDIYYLNRIGLVIFLLPILVIFTSKISKNFFVSNFQTLIFYIIVLFLF
EIVGELGAILLGMTTMSMTYFIAYCFAPTLIYNILMYLIFQKVFKKVFLES
>HMPREF9352_0003 CHAP domain protein [Streptococcus gallolyticus subsp. gallolyticus TX20005]
MKKRILSAVLVSGVTLGTAAATVNADDYDTQIAAQDAVISNLTSEQAAAQSQVDALQEQV
TSLQSQQDELEAQNAQLEAESQKLSEEIQALSSKIVARNESLKKQARSAQKTNTATSYIN
TILNSKSISDAINRVAAVREVVSANEKMLEQQEADKAAIEQKQAENQEAINTVAANKATI
EQNQAALATQQAELEAAQLNLSAQLATAEDEKASLVAQKEAAEQAAAEAAAAQAAAEAQA
QAEAEAQAASVAQAQESVENGTATVDTTTDTSSQDSTTASTDTAAATEDTSSTQQAATVT
PTATTTTSSSSSSSSASSSSSSSSSASTSSTASTSTSSSSSSSSSSSSVNTYPVGQCTWG
VKSLASWVGNNWGNANQWIASAQAAGHSVGTTPQVGAVAVWPYDGGGYGHVAYVTAVQSS
TSIQVMEANYAGNSSIGNYRGWFDPTSSTWGGGTVYYIYQ
>HMPREF9352_0004 ribose-phosphate diphosphokinase [Streptococcus gallolyticus subsp. gallolyticus TX20005]
MSYSDLKLFALSSNKELAEKVASAMGIELGKSTVRQFSDGEIQVNIEESIRGHHVFILQS
TSSPVNDNLMEILIMVDALKRASAEKISVVIPYYGYARQDRKARSREPITSKLVANMLEV
AGVDRLLTVDLHAAQIQGFFDIPVDHLMGAPLIADYFDRHGLVGDDVVVVSPDHGGVTRA
RKLAQFLQTPIAIIDKRRSVTKMNTSEVMNIIGNVKGKKCILIDDMIDTAGTICHAADAL
AEAGATAVYASCTHPVLSGPALENIEKSAIQKLVVLDTIYLSEERLIDKIEQISIAELIA
EAITRIHEKRPLSPLFEMGTAK
>HMPREF9352_0005 putative aromatic-amino-acid transaminase [Streptococcus gallolyticus subsp. gallolyticus TX20005]
MSLTNRFNKNLDKIEVSLIRQFDQSISDVPGIMKLTLGEPDFTTPDHVKEAAKAAIDANQ
SHYTGMAGLPALRQAAADFVKSKYNLSYNPDNEILVTIGATEALSATLTAILEPGDTVLL
PAPAYPGYEPIANLVGAEIVEIDTTANDFVLTPEMLEKAILEQGDKLKAVLLNYPTNPTG
VTYSREQIKALADVLKKYDIFVISDEVYSELTYNDEPHVSIAEYLPEQTILINGLSKSHA
MTGWRIGLIFAPAIFTAQLIKSHQYLVTAAATMAQFAAIEALSAGKDDALPMKVEYIKRR
DYIIDKMSALGFKIIKPDGAFYIFAKIPAGYEQDSFKFCQDFAREKAVAFIPGVAFGKYG
EGYLRLSYAASMETITTAMERLKEFMEEHAN
>HMPREF9352_0006 DNA repair protein RecO [Streptococcus gallolyticus subsp. gallolyticus TX20005]
MQTKETYGLVLYNRNYREDDKLVKIFTETNGKHMFFVKHAGKSRFNSVIQPLTVAKFILK
INDTGLSFIEDYKEVDSFKEINADLFKLSYASYVTALADAAVPDGVADPQLFAFVNKTLS
LMEEGLDYEILTNIFEIQLLERFGVSLNFHECAFCHRVGLPFDFSHKYSGLLCPEHYGKD
DYRSHLDPNVLYLVDRFQAIHFDELKTISVKPEMKRKLRLFIDDIYDNYVGLRLKSKKFI
DDLGTWGNIMK

Say that your FASTA file is a file called, say, tmp.fa.

> library(Biostrings)

> z <- readAAStringSet("tmp.fa")
> z
  A AAStringSet instance of length 6
    width seq                                               names               
[1]   254 MSLAFLFRNSGVVSAISSPIRSV...ERVVYVTSTADFSDISYVTIVGD HMPREF9352_0001 r...
[2]   171 MIKVKFYKNKYFLLLLLFLLMLI...TLIYNILMYLIFQKVFKKVFLES HMPREF9352_0002 r...
[3]   460 MKKRILSAVLVSGVTLGTAAATV...NYRGWFDPTSSTWGGGTVYYIYQ HMPREF9352_0003 C...
[4]   322 MSYSDLKLFALSSNKELAEKVAS...AEAITRIHEKRPLSPLFEMGTAK HMPREF9352_0004 r...
[5]   391 MSLTNRFNKNLDKIEVSLIRQFD...AASMETITTAMERLKEFMEEHAN HMPREF9352_0005 p...
[6]   251 MQTKETYGLVLYNRNYREDDKLV...YVGLRLKSKKFIDDLGTWGNIMK HMPREF9352_0006 D...
> alphabetFrequency(z)
      A  R  N  D C  Q  E  G H  I  L  K  M  F  P  S  T W  Y  V U O B J Z X * - +
[1,] 12  7 14 18 1  3 18 15 0 18 21 14  2  9  4 45 18 1  6 28 0 0 0 0 0 0 0 0 0
[2,]  5  1  6  3 1  3  3  7 3 20 33 12  7 22  2 13  6 0 13 11 0 0 0 0 0 0 0 0 0
[3,] 87  6 23 16 1 45 31 20 2 16 20 15  3  1  5 73 47 7 11 31 0 0 0 0 0 0 0 0 0
[4,] 33 16  9 21 3 10 21 18 9 32 30 19 10  8 11 24 15 0  7 26 0 0 0 0 0 0 0 0 0
[5,] 49 10 14 23 1 12 28 21 6 32 36 26 11 18 20 20 25 1 19 19 0 0 0 0 0 0 0 0 0
[6,] 12 10 12 21 3  5 15 13 8 15 29 22  5 20  7 13 11 1 13 16 0 0 0 0 0 0 0 0 0
     . other
[1,] 0     0
[2,] 0     0
[3,] 0     0
[4,] 0     0
[5,] 0     0
[6,] 0     0
>

Does that help?