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Chlamydiae Database version 2.0

circos
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".
Example of BLAST results
BLAST

Protein annotation view

Screenshot of the annotation page of CT_495

Alignments of target genomic regions

Genome aligments based on identified orthologs (interactive plot)

Whole genomes alignments

Circos comparative plot (interactive plot)
circos

Identification of genome(s) specific genes

Venn diagram: orthologs (interactive plot)

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
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