Recover from protein ID the corresponding nucleotide ID .

Question

[Chvatil]

Hello, does anyone know an automated way from an ID protein sequence to recover an ID and/or nucleotide sequence ?

For exemple I have the protein ID sequence :

YP_009344822.1

which is :

>YP_009344822.1 transcription associated protein [Pea leaf distortion virus]
MRSSSPSKDHYTQVPIKVQHREAKKRNRRRRVDLECGCSYFLSLNCFNHGFTHRGTHHCSSSMEWRLYLG
SSKSPLFQDPQPRQPSIHDEHGHHQDQDPIQLQPSESSGSAQVFSDLPNLDDLTPSDWSFLKSIQNPSPQ
VSHKSGCNLN

and I would like to recover its nucleotide ID : NC_033554.1

 >NC_033554.1:c1601-1149 Pea leaf distortion virus clone N36-41 segment DNA-A, complete sequence
ATGCGATCTTCATCACCCTCGAAGGACCACTATACTCAGGTTCCAATCAAAGTACAGCACAGGGAAGCGA
AGAAGCGCAACAGGAGGAGGAGAGTCGATCTTGAATGCGGGTGTTCTTATTTTCTATCTCTAAACTGCTT
CAACCATGGATTTACGCACAGGGGGACCCATCACTGCAGCTCAAGCATGGAGTGGCGCCTATATCTGGGA
AGTTCCAAATCCCCTCTATTTCAAGATCCTCAGCCACGACAACCGTCCATTCACGATGAACATGGACATC
ATCAAGATCAGGATCCAATTCAACTACAACCTTCGGAGAGCTCTGGGAGTGCACAAGTGTTTTCTGACCT
ACCGAATCTGGACGACCTTACACCCTCAGACTGGTCTTTTCTTAAAAGTATTCAAAACCCAAGTCCTCAA
GTATCTCACAAATCTGGGTGTAATCTCAATTAA

Thank you for your help.

Answer 1

[GenoMax]

Use NCBI EntrezDirect:

$ esearch -db protein -query "YP_009344822.1" | elink -target nuccore | efetch -format acc
NC_033554.1

Answer 2

[massa.kassa.sc3na]

Hi,

the most easy way I've found to obtain the nucleotide sequence for the protein with its ID is to go for efetch (from Entrez Direct).

efetch -db protein -id YP_009344822.1 -format fasta_cds_na
>lcl|NC_033554.1_cds_YP_009344822.1_1 [gene=TrAP] [locus_tag=BZL59_gp4] [db_xref=GeneID:30906012] [protein=transcription associated protein] [protein_id=YP_009344822.1] [location=complement(1149..1601)] [gbkey=CDS]
ATGCGATCTTCATCACCCTCGAAGGACCACTATACTCAGGTTCCAATCAAAGTACAGCACAGGGAAGCGA
AGAAGCGCAACAGGAGGAGGAGAGTCGATCTTGAATGCGGGTGTTCTTATTTTCTATCTCTAAACTGCTT
CAACCATGGATTTACGCACAGGGGGACCCATCACTGCAGCTCAAGCATGGAGTGGCGCCTATATCTGGGA
AGTTCCAAATCCCCTCTATTTCAAGATCCTCAGCCACGACAACCGTCCATTCACGATGAACATGGACATC
ATCAAGATCAGGATCCAATTCAACTACAACCTTCGGAGAGCTCTGGGAGTGCACAAGTGTTTTCTGACCT
ACCGAATCTGGACGACCTTACACCCTCAGACTGGTCTTTTCTTAAAAGTATTCAAAACCCAAGTCCTCAA
GTATCTCACAAATCTGGGTGTAATCTCAATTAA

And do some post-processing to obtain the header in the format you want.