P2CS-Web

Bifidobacterium longum subsp. longum ATCC 55813

Bacteria · Actinomycetota · Actinomycetes · Bifidobacteriales · Bifidobacteriaceae · Bifidobacterium

Strain: ATCC 55813

TCS census

Genome-level counts from the current P2CS annotation tables

All genes20Total predicted proteins linked to this genome record.

HK10Histidine kinase predictions in the genes table.

RR10Response regulator predictions in the genes table.

CheA0CheA-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_000003135Stable genome identifier used across P2CS views.

Genome nameBifidobacterium longum subsp. longum ATCC 55813NCBI organism name imported through the genome catalogue.

Strain / isolateATCC 55813Infraspecific name when supplied by the source assembly metadata.

Taxon ID548480NCBI taxonomic identifier linked to the imported genome catalog.

AssemblyASM313v1 · ScaffoldNo RefSeq category available for this record.

Composition2,40 Mb · 60,5% GCGenome size and GC content when available in the catalog.

External recordsPRJNA224116 · SAMN00001475Bifidobacterium longum subsp. longum ATCC 55813

Taxonomy snapshotBacteria · Actinomycetota · Actinomycetes · Bifidobacteriales · Bifidobacteriaceae · BifidobacteriumUnknown

genome_ANI

ANI and taxonomy consistency checks

Taxonomy checkOK

Best-match statusderived-species-match

Best speciesBifidobacterium longum

Best type assemblyGCA_000196555.1

Best type categorytype

Best ANI98.95%

Best qcov85,0%

Best scov84,5%

Declared assemblyGCA_000196555.1

Declared organismBifidobacterium longum subsp. longum JCM 1217

Declared categorytype

Declared ANI98.95%

genome_checkM

Completeness and contamination estimates

Completeness98,8%

Contamination0,2%

Marker setBifidobacterium longum

genome_genbank

Assembly and annotation metadata

Organism nameBifidobacterium longum subsp. longum ATCC 55813

Infraspecificstrain=ATCC 55813

WGS masterACHI00000000.1

Version statuslatest

Release typeMajor

Genome representationFull

Sequence release2009-05-05

SubmitterBaylor College of Medicine

Groupbacteria

Ungapped size2 372 858

Replicons1

Scaffolds114

Contigs140

Annotation providerBaylor College of Medicine

Annotation nameAnnotation submitted by Baylor College of Medicine

Annotation date2013-09-17

Total genes2171

Protein-coding2109

Non-coding62

Genome circular map

Circos-like overview of the selected replicon with central GC, strand-specific genes, zoomable coordinates, and TCS organization markers

GenomeGCF_000003135

RepliconNZ_GG666849.1

Length630,8 kb

Tracks542 genes · 8 TCS

Replicon

Zoom

Genes on + strand Genes on - strand HK RR CheA PP/Hpt GC% GC skew Cumulative GC skew Composition baseline

Context Orphan (2) Pair (3) Triad (0) Tetrad (0) Pentad (0) Pentad+ (0) Not in context (0)

Linear chromosome and composition views

Linear overview of the selected replicon, with strand-separated genes and composition plots aligned on the same genomic coordinate system.

Genes on + strand Genes on - strand HK RR CheA PP/Hpt

Sources

GFF: GCF_000003135.gff.gz · Sequence: GCF_000003135.1_ASM313v1_genomic.fna.gz

TCS Organization

Click a count to filter the gene list below

Orphan	Pair	Triad	Tetrad	Pentad	Pentad+	Not in context
4 (4 genes)	7 (14 genes)	0 (0 gene)	0 (0 gene)	0 (0 gene)	0 (0 gene)	2 (2 genes)

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

Gene distribution

Total proteins: 20

HK10proteins in this genome

P2CS Predicted Histidine Kinases

P2CS Predicted Histidine Kinases (10 proteins across 1 families) · Phylogenetic Tree · Data Heatmap

Genome total 10Database 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.

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.

RR10proteins in this genome

P2CS Predicted Response Regulators

P2CS Predicted Response Regulators (10 proteins across 4 families) · Phylogenetic Tree · Data Heatmap

Genome total 10Database 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.

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 genes HK RR CheA PP Orphan Pair Triad Pentad+

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.