Q1. Overview of CasPDB

CasPDB is a useful database of putative Cas proteins and Cas operons across all bacteria.In CasPDB, we collect manually curated cas proteins in Uniprot and putative cas proteins through comparing the whole proteome with multiple sequence alignments or seed alignments of cas protein families. All data in CasPDB are supported to be browsed, searched and downloaded.

Q2. Home Page Introduction

The homepage is displayed in the following Fig 1.
Fig 1:
1.Main functions of the database are provided in menu bar form (boxed in light blue).
2.A search panel accepts three types of key words:Taxomomy ID,Species name,Protein accession.
3.Abstract of the CasPDB
4.Statistic of putative cas proteins and operons and bacterium in CasPDB.
5.Link of our group and other databases contributed by our group

Q3. Search Options Introduction

The search option is displayed in Fig 2:
1.A search panel accepts three types of key words:Taxomomy ID, Species name, Protein accession.

Q4. How to read Results

Fig 3:
1.In the result page1, all entries are listed with Taxnonmy ID, Species name, Number of peotein, Exist protein cluster?, Exist Crispr locus?, Exist putative system?.
Taxnonmy ID : Official species id.
Species name : bacterium name or archaea name.
Number of peotein : The number of cas proterins in a species.
Exist protein cluster? : 'yes' means that there are clusters of Cas proteins in adjacent genomes in target species. 'no' is conversely.
Exist Crispr locus? : 'yes' means that there are crispr locus in target species. 'no' is conversely.
Exist putative system? : 'yes' means that there are CRISPR-Cas systems in target species. 'no' is conversely.
2.If you want to get more information about this specie,click species name to get in protein page.
Fig 4:
3.In the result page2, all entries are listed with CasPDB ID, Protein, Sign , Species name, Description, E-value, Length.
CasPDB ID : the rank of results
Protein name : cas protein name
Sign : different sources(0:protein from bacterium;1:protein from archaea)
Species name : the specie of bacteria or archaea
Description : the detail annotation information
E-value : the significance of possibility for a candidate cas protein
Length : the length of amino acid sequence
4.Put a tick before the number,and click button(Tick and download) you can download protein informaintion.
5.If you want to get more detail information of this protein, click protein name to get in deatil page.

Q5. Detail Page Introduction

The detail page presents the basic information of one protein, the cluster figure protein belongs and names of its co-worker, amino acid sequence of protein and putative system of species.
Fig 5:
1.Basic information: CasPDB ID, protein name, species name, description, evalue, length, sign, protein accession and CasPDB ID in cluster. Link in protein accession is to page the NCBI.
2.Figure shows the cluster target protein belongs and its members distinguish with different colors, label with sequence length.
3.Amino acid sequence of protein divide by ten as a unit to present.
4.Putative system of species.The green square graph is CRISPR locus,other colors are proteins,click figure can show you detail information of protein.

Q6. Download Page Introduction

In the download page, click file name to obtain the all putative cas proteins and operons across all bacterium and archaea

Q7. Blast CasPDB

Blast CasPDB can blast putative Cas proteins in CasPDB. The file uploaded must end with '.fna', '.fasta' or '.txt'.
Fig 7:
1.This page show the result of Blast CasPDB. Each sequence shows the best ten results.Click a result can get detail information of this protein.
2.Click Download button to download blast result file.