P2CS-Web

Two-component systems, rebuilt for exploration

Clostridioides difficile

Bacteria · Bacillota · Clostridia · Peptostreptococcales · Peptostreptococcaceae · Clostridioides

TCS census

Genome-level counts from the current P2CS annotation tables

All genes113Total predicted proteins linked to this genome record.
HK52Histidine kinase predictions in the genes table.
RR60Response regulator predictions in the genes table.
CheA1CheA-like kinase predictions in the genes table.
PP1Phosphatase predictions in the genes table.

Genome overview

Curated genome metadata from the imported catalog and Cheops-linked sources

Genome IDGCF_900688555Stable genome identifier used across P2CS views.
Taxon ID1496NCBI taxonomic identifier linked to the imported genome catalog.
Assembly7614_7#46 · ScaffoldNo RefSeq category available for this record.
Composition4,42 Mb · 28,5% GCGenome size and GC content when available in the catalog.
External recordsPRJNA224116 · SAMEA1402364Clostridioides difficile
Taxonomy snapshotBacteria · Bacillota · Clostridia · Peptostreptococcales · Peptostreptococcaceae · ClostridioidesBacteria; Bacillati; Bacillota; Clostridia; Peptostreptococcales; Peptostreptococcaceae; Clostridioides

genome_ANI

ANI and taxonomy consistency checks

Taxonomy checkOK
Best-match statusspecies-match
Best speciesClostridioides difficile
Best type assemblyGCA_001077535.2
Best type categorytype
Best ANI99.45%
Best qcov88,5%
Best scov91,1%
Declared assemblyGCA_001077535.2
Declared organismClostridioides difficile ATCC 9689 = DSM 1296
Declared categorytype
Declared ANI99.45%

genome_checkM

Completeness and contamination estimates

Completeness98,7%
Contamination5,4%
Marker setClostridium difficile

genome_genbank

Assembly and annotation metadata

Organism nameClostridioides difficile
Infraspecificstrain=lsh09
WGS masterCAADAX000000000.1
Version statuslatest
Release typeMajor
Genome representationFull
Sequence release2019-02-21
SubmitterSC
Groupbacteria
Ungapped size4 416 480
Replicons0
Scaffolds155
Contigs155
Annotation providerSC
Annotation nameAnnotation submitted by SC
Annotation date2019-02-21
Total genes4097
Protein-coding4015
Non-coding82

Genome circular map

Circos-like chromosome overview with gene and TCS coordinates

Genome annotation GFF not found for this genome.

TCS Organization

Click a count to filter the gene list below

OrphanPairTriadTetradPentadPentad+Not in context
25 (25 genes)36 (72 genes)1 (3 genes)0 (0 gene)0 (0 gene)1 (6 genes)7 (7 genes)

Not in context = predicted HK, RR, and PP genes missing from the TCS context database.

Gene distribution

Total proteins: 113

Distribution chart type
HK52proteins in this genome

P2CS Predicted Histidine Kinases

P2CS Predicted Histidine Kinases (52 proteins across 2 families) · Phylogenetic Tree · Data Heatmap

Genome total 52Database total 12 517 906Click counts to filter the genome gene list
Family distribution

Genome composition on the right, clickable family counts on the left, and a genome-vs-database radar plot.

Histidine Kinases52

Open only the HK proteins for this genome in the gene list below.

HK families2 entries
Classic51 · 98,1%CheA1 · 1,9%

Family composition

Pie, bar, or treemap view for the current genome.

Genome vs database radar

Percent of each family in this genome compared with the whole P2CS database.

RR60proteins in this genome

P2CS Predicted Response Regulators

P2CS Predicted Response Regulators (60 proteins across 9 families) · Phylogenetic Tree · Data Heatmap

Genome total 60Database total 12 774 395Click counts to filter the genome gene list
Family distribution

Genome composition on the right, clickable family counts on the left, and a genome-vs-database radar plot.

Response Regulators60

Open only the RR proteins for this genome in the gene list below.

RR families9 entries
OmpR42 · 70%LytTR9 · 15%CheY3 · 5,0%AmiR_NasR1 · 1,7%NarL1 · 1,7%NtrC1 · 1,7%PleD1 · 1,7%Spo0A1 · 1,7%unclassified1 · 1,7%

Family composition

Pie, bar, or treemap view for the current genome.

Genome vs database radar

Percent of each family in this genome compared with the whole P2CS database.

PP1proteins in this genome

P2CS Predicted PP / Hpt Proteins

P2CS Predicted PP / Hpt Proteins (1 proteins across 1 families) · Phylogenetic Tree · Data Heatmap

Genome total 1Database total 371 352Click counts to filter the genome gene list
Family distribution

Genome composition on the right, clickable family counts on the left, and a genome-vs-database radar plot.

PP / Hpt Proteins1

Open only the PP proteins for this genome in the gene list below.

PP families1 entries
HisKa1 · 100%

Family composition

Pie, bar, or treemap view for the current genome.

Genome vs database radar

Percent of each family in this genome compared with the whole P2CS database.

P2CS shortcuts

Classic entry points plus a collapsible genome protein list at the end of the page

All genesHKRRCheAPPOrphanPairTriadPentad+
Genome proteins

Full genome protein list with the same filters, grouped contexts, and links to the browser or gene detail pages.

Open this section to load the genome protein list.

Selected gene

Inline mode is active

Choose a gene from the list above to display its details below the genome sheet.