Gene detail

JS536_RS10605

Histidine kinase, Classic

Bifidobacterium sp. SO4 · GCF_018555355

Open genome Open selected cluster RefSeq

ClassHKTypeClassicLength406 aaTM0ValidatedNoCompleteYesContextpaired

Gene IDGCF_018555355#JS536_RS10605Stable P2CS identifier used across views.

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

Selected clusterHKOC_2391388Run 6 · 1 sequences · id 100% · cov 80% · representative

External referencesWP_214356917.1 · MIST4 JS536_RS10605RefSeq · MIST4

Domain signature

Compact overview inferred from the domain field

HisKA_3HATPase_c

Protein length406 aaLength used to scale native and Biotite-like views.

Annotated domains22 with usable coordinates.

Domain coverage147 / 406 aa (36.2%)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 aa406 aa

Domain-by-domain annotation2 items

1 HisKA_3#1

201-265 aa · 65 aa · 16.0% of protein

Raw tokenHisKA_3:201:0.0000000338:265:65:68

2 HATPase_c#2

322-403 aa · 82 aa · 20.2% of protein

Raw tokenHATPase_c:322:0.0000342:403:100:109

Raw architecture: HisKA_3:201:0.0000000338:265:65:68#HATPase_c:322:0.0000342:403:100:109
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_JAFEJP010000019.1::G00008

Group size22 locus tags listed below.

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

Context span13465-15508Genomic interval covered by the local TCS group.

Identifiers

Old locus tagJS536_10600RefSeq proteinWP_214356917.1

Context group IDGCF_018555355::NZ_JAFEJP010000019.1::G00008

Context members

JS536_RS10605JS536_RS10610

Partner locus tags

JS536_RS10605JS536_RS10610

Partner old locus tags

JS536_10600JS536_10605

Partner protein IDs

WP_214356917.1 WP_346427481.1

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_214356917.1.

Genomic coordinates

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

Current locus tagJS536_RS10605Primary locus identifier stored in the genes table.

Old locus tagJS536_10600Legacy locus tag recovered from the local context mapping.

Contig / repliconNZ_JAFEJP010000019.1Sequence record reported by the local genomic context database.

Genomic interval13 465-14 685 nt1 221 nt · Forward (+)

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

Local TCS group span13 465-15 508 ntGCF_018555355::NZ_JAFEJP010000019.1::G00008

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_JAFEJP010000019.1::G00008

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_JAFEJP010000019.1All displayed genes belong to this local TCS context.

Neighborhood span13 465-15 508 nt2 044 nt

Members21 current focus gene

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

13 465 nt15 508 nt

+-JS536_RS10605 JS536_RS10610

Neighborhood gene cards

2 genes in the current local neighborhood.

JS536_RS10605GCF_018555355#JS536_RS10605

HKClassicCurrent focus

13 465-14 685 nt · Forward (+)

Old locus JS536_10600RefSeq WP_214356917.1

Open current gene

JS536_RS10610GCF_018555355#JS536_RS10610

RRNarL

14 849-15 508 nt · Forward (+)

Old locus JS536_10605RefSeq WP_346427481.1

Open gene

Clusters

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

Available memberships1 cluster

HKOC_2391388HK

Run 61 sequencesid 100%cov 80%

PFAM HisKA_3

Current gene is the representative sequence.

Selected clusterHKOC_2391388Run 6 · HK · 1 sequences

Representative sequenceGCF_018555355#JS536_RS10605The 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_2391388

Simplified PFAM architecture for HKOC_2391388

PFAM domain coverage: 69 / 406 aa (17.0%)

1 aa406 aa

HisKA_3

Simplified architecture: HisKA_3
Raw architecture: HisKA_3[200-268]
Domain count: 1
Matched identifier: HKOC_2391388
Positioned domains: HisKA_3 200-268

Cluster members and taxonomy

Representative gene: GCF_018555355#JS536_RS10605

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

Related genes

Preview from the same derived genome key