A sequence pattern for the destruction motif was suggested as RxxLxxxxN/Q, where x is any amino acid, R is Arginine L is Leucine and N/Q is Asparagine or Glutamine. Searching with this sequence pattern retrieves many false positive results, for example many hits from prokaryotic sequences. We defined the destruction box motif more accurately so that it can be used for searching for new putative D-box motifs.
The D-box Finder server identifies putative Destruction box motifs in submitted sequences. The identification is done by comparing the query sequence with blocks representing the D-box motifs from cyclin A, cyclin B, securin, geminin and CDC6 protein families. Blocks are short multiply aligned ungapped conserved segments . The D-box blocks contain conserved regions that include established distruction box motifs from different protein families . They include the known D-box pattern sequence and conserved positions upstream and downstream to it.
D-box motifs are typically distinct between different protein families. A D-box block from one family does not always identify the D-box motifs from other families at a significant level, making the identification of a new putative D-box motifs a difficult task. D-box identification by this server is recommended for known APC substrates or proteins suspected as targets of D-box dependent degradation. We recommend also analyzing the putative D-box motif by other methods, such as analysis of the conservation of this motif in other homologous proteins (for example, by Blast searches). The final proof is, of course, experimental, verifying the motif as a functional destruction box. This server can be useful in selecting targets for experimental analysis of D-box motifs .
The output is divided into 3 parts : Heading, Summary and Details.
Heading
Query = Description line from query sequence.
Size = Number of amino acids for protein query or base pairs for DNA query. Be sure this number is correct before interpreting your results.
Blocks searched =Number of blocks searched against the query. The searched blocks database of the server contains five D-box blocks from different families.
Alignments done =Number of alignments done between query and blocks searched. this number is used to determine the expected value for each hit.
Cutoff expected value = The statistical significance threshold for reporting hits . The default value is 1, meaning that one hit is expected to be found merely by chance.
Summary
This part summarizes the search results. There is one line description for each hit against the searched blocks database. The hits are sorted by their E-value. Since each family is represented by only one D-box block the combined E-value is the E-value for a single block hit.
Details
Detailed information is printed for each hit, including alignments with the most similar sequence in each block.
Frame: 0 for protein query, or 1,2,3,-1,-2,-3 for DNA query. Negative numbers represent a reverse DNA strand.
Location: Location of the segment similar to the block within query sequence in amino acids for protein or base pairs from 5' to 3' on the DNA query. If the hit was found on a reverse DNA strand the location is from 5' to 3' on that strand, that is from the 3' end of the forward strand.
Block E-value: Expected number of times the score this hit could be seen by chance in all alignments that were done (the number of the alignments is written in the Heading part).
Alignments: This part shows an alignment of the identified query sequence segment with the most similar motif from the block hit. Identical amino acids are joined by a line ( | ). Query amino acids different from those in the motif are shown in uppercase if they occur in that position in any motif from that block. Thus, an uppercase amino acid occurs at some other motif in this position, and a lowercase amino acid was never observed in this position in any motif of the block.