An experimentally based computer search identifies unstructured membrane-binding sites in proteins: Application to class-I myosins, PAKs and CARMIL Hanna Brzeska, Jake Guag, Kirsten Remmert, Susan Chacko and Edward D. Korn J. Biol. Chem., 285: 5738-5747 (2010)
Run EMBOSS pepinfo
EMBOSS pepinfo documentation
One or more sequences can be entered into the program by
ncbigp NCBI's Genpept - protein translations of Genbank sequences ncbigpnew new entries in NCBI's Genpept since the last release genpept NCI-Frederick Genpept gpnew new entries in NCI-Frederick Genpept since the last release refseqaa NCBI's Refseq protein database uniprot includes Swissprot and Tremb
To find Genbank or GI or Refseq protein IDs, Go to the NCBI website, select 'Protein' database, and type in a search term. Save the locus names (e.g. NP_731074, ACL83472) or GI numbers (e.g. 221378052) of your desired proteins, and paste them in the BH-search box.
To find Swissprot/Trembl IDs, go to The Expasy Swissprot site and type in a search term. Save the Uniprot accession number (e.g. P01542) or entry name (e.g. CRAM_CRAAB) of your desired proteins, and paste them in the BH-search box.
Swissprot/Trembl are produced by the Uniprot consortium.
Cut&pasted sequences or uploaded sequence files can be in any common format: Fasta, Genbank, Swissprot, EMBL. Input sequences are first processed by the EMBOSS Seqret program to convert them into Fasta format. Note that 'Plain' or 'Raw' format will not work for multiple sequences, since there is no way to tell where one sequence ends and another begins. Therefore, if you want to run multiple sequences at once, it is recommended that you use Fasta, Genbank, or Swissprot formats.
Sample file of Fasta-format sequences
Sample file of Genbank-format sequences
Sample file of Swissprot-format sequences
Raw/Plain Sequence data: These are sequences that are not in a standard format, and for which you have only the actual sequence data. For example, if you have sequence data like this:
MTIAITDVVLRDAHQSLFATRLRLDDMLPIAAALDDVGYGSLECWGGATFDACIRFLGEDPWLRLRELKK AMPKTPLQMLLRGQNLLGYRHYADDVVERFVERAVKNGMDVFRVFDAMNDPRNMKAALQAVRSHGAHAQG TLSYTTSPAHTLQTWLDLTEQLLETGVDSIAIKDMSGILTPMAAYELVSEIKKRFEVRLHLHCHATTGMA EMALLKAIEAGVDGVDTAISSMSATYGHPATEALVATLAGTEHDTGLDILKLENIAAYFREVRKKYHAFE
To make this sequence usable, it is easiest to make it Fasta format. Add a '>' and any desired text on a line before the sequence, as below:
>test1 this is my sequence MTIAITDVVLRDAHQSLFATRLRLDDMLPIAAALDDVGYGSLECWGGATFDACIRFLGEDPWLRLRELKK AMPKTPLQMLLRGQNLLGYRHYADDVVERFVERAVKNGMDVFRVFDAMNDPRNMKAALQAVRSHGAHAQG TLSYTTSPAHTLQTWLDLTEQLLETGVDSIAIKDMSGILTPMAAYELVSEIKKRFEVRLHLHCHATTGMA EMALLKAIEAGVDGVDTAISSMSATYGHPATEALVATLAGTEHDTGLDILKLENIAAYFREVRKKYHAFE
Word documents: Word is not a sequence format, and no program can read a sequence in Word format. Sequences in an uploaded Word document will fail.
Parameter values used by various methods:
K&D: Kyte J, Doolittle RF A simple method for displaying the hydropathic character of a protein. J Mol Biol 1982 May 5;157(1):105-132
OMH: Sweet RM, Eisenberg D Correlation of sequence hydrophobicities measures similarity in three-dimensional protein structure. J Mol Biol 1983 Dec 25;171(4):479-488
Consensus: Eisenberg D, Weiss RM, Terwilliger TC. The helical hydrophobic moment: a measure of the amphiphilicity of a helix. Nature 1982 Sep 23;299(5881):371-4
W&W: Wimley WC, White SH. Experimentally determined hydrophobicity scale for proteins at membrane interfaces. Nature Structural Biology 1996, October 10; 3; 842-848. Hydropathy plots with Wimley White parameters can be run at the website of the Stephen White laboratory
BH: Brzeska H, Guag J, Remmert K, Chacko S and Korn ED. An experimentally based computer search identifies unstructured membrane-binding sites in proteins: Application to class-I myosins, PAKs and CARMIL J. Biol. Chem., 285: 5738-5747 (2010)
At the end of the page there are links to a file with all the Fasta-format sequences, a file with all the concatenated raw outputs, and a file with all the outputs in Excel CSV format. If you have uploaded a parameter file or defined your own parameters, the parameter file can also be saved for future runs. The parameters used for this run are also displayed.
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