{% include "chlamdb/menu.html" %}
{% if type == 'cog'%}
{{ fam }}
{% elif type == 'pfam' %}
{{ fam }}
{% elif type == 'ko' %}
{{ fam }}
{% endif %}
{% if no_match %}
{{fam}} not present in the database
{% else %}
Help to interpret the results
Three outputs have been generated:
General: this result contains the description and frequency of the selected
{% if type == 'cog'%}
COG entry
{% elif type == 'ko' %}
Kegg Ortholog
{% elif type == 'pfam' %}
Pfam domain
{% endif %}
{{ fam }}, of which KO pathways and KO modules it is part. Additionally, its occurence in the database is reported.
Proteins list: list of occurences of the
{% if type == 'ko'%}
COG entry
{% elif type == 'ko' %}
Kegg Ortholog
{% elif type == 'pfam' %}
Pfam domain
{% endif %}
within the database. {{ all_locus_data|length }} occurences are identified.
The table reports the orthogroup, the organism in which each occurrence has been found, and the locus tag enriched by start and stop position, strand, gene name and product.
Clicking on the Ortohgroup name or locus you will be redirected to further info.
Profiles: Phylogenetic tree annotated with
- the presence of the
{% if type == 'cog'%}
COG entry(ies)
{% elif type == 'ko' %}
Kegg Ortholog(s)
{% elif type == 'pfam' %}
Pfam domain(s)
{% endif %} of interest within all the genomes of the database (first column)
- the size of the orthogroup(s) in which the reported
{% if type == 'cog'%}
COG entry
{% elif type == 'ko' %}
Ko entry
{% elif type == 'pfam' %}
Pfam domain
{% endif %} has been clustered.
In red the {{type}} with positive hit(s) in the corresponding genome.
In green the discrepencies between orthogroup clustering and {{type}} prediction.
Green homologs (same orthogroup) are not positive hit(s) for the considered {{type}}.
Variations within orthogroups may be due to the clustering of multi domain proteins or because of erroneous homolog clustering or {{type}} prediction.
Description
{% if type == 'pfam' %}
External link |
{{ fam }} |
{% elif type == 'interpro' %}
External link |
{{ fam }} |
{% elif type == 'ko' %}
External link |
{{ fam }} |
{% elif type == 'EC' %}
External link |
{{ fam }} |
{% endif %}
{% if type == 'EC' %}
{% for key, value in info%}
{{key}} |
{% if key == "prosite"%}
{{value}} |
{% else %}
{{value}} |
{% endif %}
{% endfor %}
{{key}} |
{{value}} |
{% elif type == 'ko'%}
Accession |
{{ fam }} |
Description |
{{ ko_desc }} |
{% elif fam_interpro %}
Signature accession |
{% if type == "PANTHER" %}
{{ info.0 }} |
{% elif type == "CDD" %}
{{ info.0 }} |
{% elif type == "Pfam" %}
{{ info.0 }} |
{% elif type == "PRINTS" %}
{{ info.0 }} |
{% elif type == "TIGRFAM" %}
{{ info.0 }} |
{% elif type == "Hamap" %}
{{ info.0 }} |
{% elif type == "Gene3D" %}
{{ info.0 }} |
{% elif type == "SUPERFAMILY" %}
{{ info.0 }} |
{% elif type == "SMART" %}
{{ info.0 }} |
{% elif type == "ProSitePatterns" %}
{{ info.0 }} |
{% else %}
{{ info.0 }} {{ info.1 }} |
{% endif %}
{% if info.1 != "0" %}
Signature description |
{{ info.1 }} |
{% else %}
Signature description |
N/A |
{% endif %}
{% elif type == "cog" %}
Description |
{{ info.1 }} |
Function(s) |
{{info.0|safe}} |
{% else %}
Description |
{{ info.0 }} {{ info.1 }} |
{% endif %}
{% if type == 'ko'%}
KO part of {{pathway_data|length }} pathways
{% if pathway_data|length > 0 %}
{% for path in pathway_data %}
{{path|safe}} |
{% endfor %}
{% endif %}
KO part of {{module_data|length }} modules
{% if module_data|length > 0 %}
{% for path in module_data %}
{{path.0|safe}} |
{{path.1}} |
{{path.2}} |
{% endfor %}
{% endif %}
{% endif %}
{% if type == 'EC'%}
EC part of {{pathway_data|length }} pathways
{% if pathway_data|length > 0 %}
{% for path in pathway_data %}
{{path.0}} |
{{path.1}} |
{% endfor %}
{% endif %}
{% if associated_ko|length > 0 %}
Kegg Orthologs
Accession |
Description |
Frequency in the database |
{% for ko in associated_ko %}
{% with ko2freq|keyvalue:ko.0 as freq%}
{% if freq > 0%}
{{ko.0}} |
{{ko.1}} |
{{ freq }} |
{% else %}
{{ko.0}} |
{{ko.1}} |
- |
{% endif %}
{% endwith %}
{% endfor %}
{% endif %}
{% endif %}
Occurence in the database
{{ fam }} is associated with {{ all_locus_data|length }} different proteins (see tab "Protein list" and "Profile") |
The {{ all_locus_data|length }} proteins are classified into {{ group_count|length }} different orthogroup(s) |
{% for group in group_count %}
- {{group|safe}}
{% endfor %}
# |
Orthogroup |
Locus |
Start |
Stop |
S. |
Gene |
Product |
Organism |
{% for values in all_locus_data %}
{{values.0}} |
{{values.1|safe}} |
{{values.2}} |
{{values.4}} |
{{values.5}} |
{{values.6}} |
{{values.7}} |
{{values.8}} |
{{values.9}} |
{% endfor %}
{% endif %}