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Candidatus Deferrimicrobium sp.

Bacteria · Candidatus Deferrimicrobiota · Candidatus Deferrimicrobia · Candidatus Deferrimicrobiales · Candidatus Deferrimicrobiaceae · Candidatus Deferrimicrobium

TCS census

Genome-level counts from the current P2CS annotation tables

All genes83Total predicted proteins linked to this genome record.
HK41Histidine kinase predictions in the genes table.
RR42Response regulator predictions in the genes table.
CheA1CheA-like kinase predictions in the genes table.
PP0Phosphatase predictions in the genes table.

Genome overview

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

Genome IDGCF_036396855Stable genome identifier used across P2CS views.
Taxon ID3060586NCBI taxonomic identifier linked to the imported genome catalog.
AssemblyASM3639685v1 · ContigNo RefSeq category available for this record.
Composition2,56 Mb · 65,0% GCGenome size and GC content when available in the catalog.
External recordsPRJNA224116 · SAMN37960555Candidatus Deferrimicrobium sp.
Taxonomy snapshotBacteria · Candidatus Deferrimicrobiota · Candidatus Deferrimicrobia · Candidatus Deferrimicrobiales · Candidatus Deferrimicrobiaceae · Candidatus DeferrimicrobiumBacteria; None; Candidatus Deferrimicrobiota; Candidatus Deferrimicrobia; Candidatus Deferrimicrobiales; Candidatus Deferrimicrobiaceae; Candidatus Deferrimicrobium

genome_ANI

ANI and taxonomy consistency checks

Taxonomy checkOK
Best-match statusgenus-match
Best speciesCandidatus Deferrimicrobium borealis
Best type assemblyGCA_023617515.1
Best type categorysuspected-type
Best ANI91.15%
Best qcov66,3%
Best scov63,4%
Declared assemblyno-type
Declared categoryno-type
Excluded from RefSeqderived from metagenome

genome_checkM

Completeness and contamination estimates

Completeness94,8%
Contamination1,7%
Marker setBacteria

genome_genbank

Assembly and annotation metadata

Organism nameCandidatus Deferrimicrobium sp.
WGS masterDASWKA000000000.1
Version statuslatest
Release typeMajor
Genome representationFull
Sequence release2024-02-05
SubmitterZhejiang University
Groupbacteria
Ungapped size2 557 095
Replicons0
Scaffolds153
Contigs153
Annotation providerNCBI
Annotation nameNCBI Prokaryotic Genome Annotation Pipeline (PGAP)
Annotation date2024-01-12
Total genes2499
Protein-coding2446
Non-coding47
PubMed37951952

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
31 (31 genes)19 (38 genes)3 (9 genes)0 (0 gene)0 (0 gene)0 (0 gene)5 (5 genes)

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

Gene distribution

Total proteins: 83

Distribution chart type
HK41proteins in this genome

P2CS Predicted Histidine Kinases

P2CS Predicted Histidine Kinases (41 proteins across 4 families) · Phylogenetic Tree · Data Heatmap

Genome total 41Database 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 Kinases41

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

HK families4 entries
Classic28 · 68,3%Hybrid11 · 26,8%CheA1 · 2,4%Unorthodox1 · 2,4%

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.

RR42proteins in this genome

P2CS Predicted Response Regulators

P2CS Predicted Response Regulators (42 proteins across 11 families) · Phylogenetic Tree · Data Heatmap

Genome total 42Database 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 Regulators42

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

RR families11 entries
NtrC14 · 33,3%unclassified9 · 21,4%CheY4 · 9,5%PrrA4 · 9,5%RpfG4 · 9,5%NarL2 · 4,8%CheB1 · 2,4%OmpR1 · 2,4%PilB1 · 2,4%PleD1 · 2,4%PleD_VieA1 · 2,4%

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.

PP0proteins in this genome

P2CS Predicted PP / Hpt Proteins

P2CS Predicted PP / Hpt Proteins (0 proteins across 0 families) · Phylogenetic Tree · Data Heatmap

Genome total 0Database total 0Click 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.

No pp / hpt proteins were predicted for this genome.

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.