Gene detail

JS536_RS04660

Histidine kinase, Classic

Bifidobacterium sp. SO4 · GCF_018555355

Open genome Open selected cluster RefSeq

ClassHKTypeClassicLength462 aaTM0ValidatedNoCompleteYesContextpaired

Gene IDGCF_018555355#JS536_RS04660Stable P2CS identifier used across views.

GenomeGCF_018555355Bacteria; Bacillati; Actinomycetota; Actinomycetes; Bifidobacteriales; Bifidobacteriaceae; Bifidobacterium

Selected clusterHKOC_1813436Run 6 · 1 sequences · id 100% · cov 80% · representative

External referencesWP_214355965.1 · MIST4 JS536_RS04660RefSeq · MIST4

Domain signature

Compact overview inferred from the domain field

HisKA_3HATPase_c

Protein length462 aaLength used to scale native and Biotite-like views.

Annotated domains22 with usable coordinates.

Domain coverage167 / 462 aa (36.1%)Merged over positioned domains only.

Domain description1 HisKA_3,1 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 aa462 aa

Domain-by-domain annotation2 items

1 HisKA_3#1

234-297 aa · 64 aa · 13.9% of protein

Raw tokenHisKA_3:234:1.42e-16:297:64:68

2 HATPase_c#2

344-446 aa · 103 aa · 22.3% of protein

Raw tokenHATPase_c:344:0.0000000423:446:108:109

Raw architecture: HisKA_3:234:1.42e-16:297:64:68#HATPase_c:344:0.0000000423:446:108:109
Domain description: 1 HisKA_3,1 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_018555355::NZ_JAFEJP010000004.1::G00020

Group size22 locus tags listed below.

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

Context span136172-138339Genomic interval covered by the local TCS group.

Identifiers

Old locus tagJS536_04655RefSeq proteinWP_214355965.1

Context group IDGCF_018555355::NZ_JAFEJP010000004.1::G00020

Context members

JS536_RS04660JS536_RS04665

Partner locus tags

JS536_RS04660JS536_RS04665

Partner old locus tags

JS536_04655JS536_04660

Partner protein IDs

WP_214355965.1 WP_214355966.1

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_214355965.1.

Genomic coordinates

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

Current locus tagJS536_RS04660Primary locus identifier stored in the genes table.

Old locus tagJS536_04655Legacy locus tag recovered from the local context mapping.

Contig / repliconNZ_JAFEJP010000004.1Sequence record reported by the local genomic context database.

Genomic interval136 172-137 560 nt1 389 nt · Forward (+)

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

Local TCS group span136 172-138 339 ntGCF_018555355::NZ_JAFEJP010000004.1::G00020

Quick actions

Open genome Search genes in genome

Local neighborhood

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

GCF_018555355::NZ_JAFEJP010000004.1::G00020

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_JAFEJP010000004.1All displayed genes belong to this local TCS context.

Neighborhood span136 172-138 339 nt2 168 nt

Members21 current focus gene

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

136 172 nt138 339 nt

+-JS536_RS04660 JS536_RS04665

Neighborhood gene cards

2 genes in the current local neighborhood.

JS536_RS04660GCF_018555355#JS536_RS04660

HKClassicCurrent focus

136 172-137 560 nt · Forward (+)

Old locus JS536_04655RefSeq WP_214355965.1

Open current gene

JS536_RS04665GCF_018555355#JS536_RS04665

RRNarL

137 557-138 339 nt · Forward (+)

Old locus JS536_04660RefSeq WP_214355966.1

Open gene

Clusters

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

Available memberships1 cluster

HKOC_1813436HK

Run 61 sequencesid 100%cov 80%

PFAM HisKA_3

Current gene is the representative sequence.

Selected clusterHKOC_1813436Run 6 · HK · 1 sequences

Representative sequenceGCF_018555355#JS536_RS04660The current gene is the representative for this cluster.

PFAM architectureHisKA_31 domain in the representative PFAM annotation.

Open in cluster search

PFAM architecture for HKOC_1813436

Simplified PFAM architecture for HKOC_1813436

PFAM domain coverage: 66 / 462 aa (14.3%)

1 aa462 aa

HisKA_3

Simplified architecture: HisKA_3
Raw architecture: HisKA_3[234-299]
Domain count: 1
Matched identifier: HKOC_1813436
Positioned domains: HisKA_3 234-299

Cluster members and taxonomy

Representative gene: GCF_018555355#JS536_RS04660

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

Genome taxonomy

Unknown

Taxonomy recordUnknownTaxon ID 2 809 030 · GCF_018555355

AssemblyASM1855535v1 · Contighaploid

Genome composition2 912 164 bp · 63,0% GCBifidobacterium sp. SO4

Signal transduction countsGenes 42 · HK 15 · RR 25CheA 0 · PP 2

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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