{% include "chlamdb/menu.html" %}
Example of BLAST results
Screenshot of the annotation page of CT_495
Genome aligments based on identified orthologs (interactive plot)
Circos comparative plot (interactive plot)
Venn diagram: orthologs (interactive plot)
Chlamydiae Database version 2.0
Help page under construction. Contact trestan.pillonel[@]chuv.ch if you have suggestions, problems or questions.
Website tutorial
Search for a protein of interest
The following protein accessions can be used to search the database:
Name | Example |
---|---|
Genbank locus tag | wcw_1594 |
Genbank protein accession | ADI38940.1 |
RefSeq locus tag | WCW_RS07680 |
RefSeq protein accession | WP_013182646.1 |
UniParc accession | UPI0001D5C1DD |
UniProtKB-Accession | D6YS95 |
UniProtKB-ID | D6YS95_WADCW |
Accessions from KEGG, COG, Pfam and InterPro can also be searched to retreive the list of proteins with the corresponding annotation:
Accession type | Example | Description |
---|---|---|
KEGG ortholog | K00844 | hexokinase [EC:2.7.1.1] |
COG | COG0333 | Ribosomal protein L32 |
PFAM | PF06723 | MreB/Mbl protein |
InterPro | IPR004753 | Cell shape determining protein MreB |
KEGG modules | M00023 | Amino acid metabolism |
Kegg pathways | map00400 | Phenylalanine, tyrosine and tryptophan biosynthesis |
It's also possible to seach for a gene or product name
It's also possible to browse genomes tables from links listed in the home page table (column: Browse online)
BLAST interface
A BLAST interface is also available for homology search. You can access it from the left vertical menu under "Search".
Protein annotation view
Alignments of target genomic regions
Whole genomes alignments
Identification of genome(s) specific genes
Protein-Protein Interactions
Methods
Source of the data -- ChlamDB Version 2.0
Database name | Version |
---|---|
UniprotKB | 2019_03 |
TCDB | June 2019 |
RefSeq | 90 |
CDD (COG) | v3.17 |
InterPro | InterProScan 5.35-74.0 |
Softwares
Software name | Version |
---|---|
FastTree | 2.1.10 |
Diamond | 0.9.24 |
OrthoFinder | 2.2.7 |
BLAST | 2.7.1 |
CheckM | 1.0.12 |
KoFamScan | 2019/4/9 |
Mafft | 7.407 |