Gene detail

RY67_RS05525

Histidine kinase, Classic

Bifidobacterium longum subsp. infantis · GCF_001281305

Open genome Open selected cluster RefSeq

ClassHKTypeClassicLength345 aaTM0ValidatedNoCompleteYesContextpaired

Gene IDGCF_001281305#RY67_RS05525Stable P2CS identifier used across views.

GenomeGCF_001281305Bacteria; Bacillati; Actinomycetota; Actinomycetes; Bifidobacteriales; Bifidobacteriaceae; Bifidobacterium

Selected clusterHKOC_2819407Run 6 · 2 sequences · id 100% · cov 80% · representative

External referencesWP_060620622.1 · MIST4 RY67_RS05525RefSeq · MIST4

Domain signature

Compact overview inferred from the domain field

HisKAHATPase_c

Protein length345 aaLength used to scale native and Biotite-like views.

Annotated domains22 with usable coordinates.

Domain coverage170 / 345 aa (49.3%)Merged over positioned domains only.

Domain description1 HisKA,1 HATPase_cSummary string stored in the genes table.

Signal peptideUnavailableNo TMPRED prediction file matched this gene.

Transmembrane helicesUnavailableConfigure [protein_features] tmpred_root_dir to enable this annotation.

Complete domain annotations

Domain view

Native Biotite-like

Native P2CS viewFrontend rendering from the parsed domain string and TMPRED protein features.

1 aa345 aa

Domain-by-domain annotation2 items

1 HisKA#1

123-188 aa · 66 aa · 19.1% of protein

Raw tokenHisKA:123:0.00000000287:188:66:64

2 HATPase_c#2

234-337 aa · 104 aa · 30.1% of protein

Raw tokenHATPase_c:234:2.15e-29:337:104:109

Raw architecture: HisKA:123:0.00000000287:188:66:64#HATPase_c:234:2.15e-29:337:104:109
Domain description: 1 HisKA,1 HATPase_c
TM description: N/A
TMPRED source: No TMPRED file loaded
TMPRED segments: N/A
Complete: Yes

Context mapping

Resolved via p2cs_tcs_context.db when a locus tag match exists

Context labelpairedGCF_001281305::NZ_CP010411.1::G00010

Group size22 locus tags listed below.

HK / RR1 / 1Counts resolved for the local TCS neighborhood.

Context span1303505-1305237Genomic interval covered by the local TCS group.

Identifiers

Old locus tagRY67_1187RefSeq proteinWP_060620622.1

Context group IDGCF_001281305::NZ_CP010411.1::G00010

Context members

RY67_RS05520RY67_RS05525

Partner locus tags

RY67_RS05520RY67_RS05525

Partner old locus tags

RY67_1186RY67_1187

Partner protein IDs

WP_060620621.1 WP_060620622.1

External references

Resolved via p2cs_annexes.db when the RefSeq protein is present in the annex table

No UniProt / GO / PubMed mapping was found for WP_060620622.1.

Genomic coordinates

Resolved via p2cs_tcs_context.db when the current locus tag is present in the local context table

Current locus tagRY67_RS05525Primary locus identifier stored in the genes table.

Old locus tagRY67_1187Legacy locus tag recovered from the local context mapping.

Contig / repliconNZ_CP010411.1Sequence record reported by the local genomic context database.

Genomic interval1 304 200-1 305 237 nt1 038 nt · Forward (+)

StrandForward (+)Strand sign follows the local context database convention.

Local TCS group span1 303 505-1 305 237 ntGCF_001281305::NZ_CP010411.1::G00010

Quick actions

Open genome Search genes in genome

Local neighborhood

Graphical neighborhood resolved from the local TCS context group on the current contig

GCF_001281305::NZ_CP010411.1::G00010

Graphic view

Compact Biotite-like

Zoom

Full window Focus gene

Compact keeps a quick overview. Biotite-like switches to a coordinate-aware biological layout with strand and zoom.

Context labelpairedNeighborhood members are ordered by genomic coordinates.

Contig / repliconNZ_CP010411.1All displayed genes belong to this local TCS context.

Neighborhood span1 303 505-1 305 237 nt1 733 nt

Members21 current focus gene

Local TCS group mapArrow direction follows strand. The current gene is highlighted with a stronger outline.

1 303 505 nt1 305 237 nt

+-RY67_RS05520 RY67_RS05525

Neighborhood gene cards

2 genes in the current local neighborhood.

RY67_RS05520GCF_001281305#RY67_RS05520

RROmpR

1 303 505-1 304 191 nt · Forward (+)

Old locus RY67_1186RefSeq WP_060620621.1

Open gene

RY67_RS05525GCF_001281305#RY67_RS05525

HKClassicCurrent focus

1 304 200-1 305 237 nt · Forward (+)

Old locus RY67_1187RefSeq WP_060620622.1

Open current gene

Clusters

CD-HIT memberships and selected cluster details for the current gene class

Available memberships1 cluster

HKOC_2819407HK

Run 62 sequencesid 100%cov 80%

PFAM HisKA + HATPase_c

Current gene is the representative sequence.

Selected clusterHKOC_2819407Run 6 · HK · 2 sequences

Representative sequenceGCF_001281305#RY67_RS05525The current gene is the representative for this cluster.

PFAM architectureHisKA + HATPase_c2 domains in the representative PFAM annotation.

Open in cluster search

PFAM architecture for HKOC_2819407

Simplified PFAM architecture for HKOC_2819407

PFAM domain coverage: 170 / 345 aa (49.3%)

1 aa345 aa

HisKAHATPase_c

Simplified architecture: HisKA + HATPase_c
Raw architecture: HisKA[125-188] | HATPase_c[234-339]
Domain count: 2
Matched identifier: HKOC_2819407
Positioned domains: HisKA 125-188 ; HATPase_c 234-339

Cluster members and taxonomy

Representative gene: GCF_001281305#RY67_RS05525

Sankey plot built from the taxonomy of all members in the selected cluster.

Genome taxonomy

Unknown

Taxonomy recordUnknownTaxon ID 1 682 · GCF_001281305

AssemblyASM128130v1 · Complete Genomehaploid

Genome composition2 578 115 bp · 59,5% GCBifidobacterium longum subsp. infantis

Signal transduction countsGenes 40 · HK 13 · RR 24CheA 0 · PP 3

Ranked taxonomy7 ranked levels available

SuperkingdomBacteriaKingdomBacillatiPhylumActinomycetotaClassActinomycetesOrderBifidobacterialesFamilyBifidobacteriaceaeGenusBifidobacterium

Lineage path7 lineage nodes

1Bacteria2Bacillati3Actinomycetota4Actinomycetes5Bifidobacteriales6Bifidobacteriaceae7Bifidobacterium

Open genome Search genes in genome Search HK genes NCBI assembly files

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