Gene detail

HMPREF0175_RS02665

Histidine kinase, Classic

Bifidobacterium longum subsp. longum ATCC 55813 · GCF_000003135

Open genome Open selected cluster RefSeq

ClassHKTypeClassicLength410 aaTM0ValidatedNoCompleteYesContextpaired

Gene IDGCF_000003135#HMPREF0175_RS02665Stable P2CS identifier used across views.

GenomeGCF_000003135Unknown

Selected clusterHKOC_2354145Run 6 · 6 sequences · id 100% · cov 80% · representative

External referencesWP_007054471.1 · MIST4 HMPREF0175_RS02665RefSeq · MIST4

Domain signature

Compact overview inferred from the domain field

HisKA_3HATPase_c

Protein length410 aaLength used to scale native and Biotite-like views.

Annotated domains22 with usable coordinates.

Domain coverage136 / 410 aa (33.2%)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 aa410 aa

Domain-by-domain annotation2 items

1 HisKA_3#1

201-265 aa · 65 aa · 15.9% of protein

Raw tokenHisKA_3:201:0.0000000594:265:65:68

2 HATPase_c#2

322-392 aa · 71 aa · 17.3% of protein

Raw tokenHATPase_c:322:0.0000324:392:86:109

Raw architecture: HisKA_3:201:0.0000000594:265:65:68#HATPase_c:322:0.0000324:392:86:109
Domain description: 1 HisKA_3,1 HATPase_c
TM description: N/A
TMPRED source: No TMPRED file loaded
TMPRED segments: N/A
Complete: Yes

Protein sequence

On-demand local amino-acid sequence in FASTA format

Context mapping

Resolved via p2cs_tcs_context.db when a locus tag match exists

Context labelpairedGCF_000003135::NZ_GG666853.1::G00009

Group size22 locus tags listed below.

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

Context span143270-145262Genomic interval covered by the local TCS group.

Identifiers

Old locus tagHMPREF0175_2065RefSeq proteinWP_007054471.1

Context group IDGCF_000003135::NZ_GG666853.1::G00009

Context members

HMPREF0175_RS02670HMPREF0175_RS02665

Partner locus tags

HMPREF0175_RS02670HMPREF0175_RS02665

Partner old locus tags

HMPREF0175_2064HMPREF0175_2065

Partner protein IDs

WP_007056206.1 WP_007054471.1

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_007054471.1.

Genomic coordinates

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

Current locus tagHMPREF0175_RS02665Primary locus identifier stored in the genes table.

Old locus tagHMPREF0175_2065Legacy locus tag recovered from the local context mapping.

Contig / repliconNZ_GG666853.1Sequence record reported by the local genomic context database.

Genomic interval144 030-145 262 nt1 233 nt · Reverse (-)

StrandReverse (-)Strand sign follows the local context database convention.

Local TCS group span143 270-145 262 ntGCF_000003135::NZ_GG666853.1::G00009

Quick actions

Open genome Search genes in genome

Genome neighborhood

Gene-centered window parsed directly from the configured gzipped GFF annotation

GCF_000003135 · NZ_GG666853.1

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.

Centered locusHMPREF0175_RS0266511 genes displayed around the current focus.

Configured flank5 upstream / downstreamWindow size loaded from config.ini.

Annotation sourceGCF_000003135.gff.gzResolved as <gff_root_dir>/<genome_id>/<genome_id>.gff.gz when available.

View modeGene-centered orderThis track keeps the current gene in the middle of the context window when possible.

Gene-centered contextFive upstream and five downstream genes can be shown when the configured flank count is set to 5.

Current geneHKRROther P2CSOutside P2CS

HMPREF0175_RS02690HMPREF0175_RS02690

HMPREF0175_RS02685HMPREF0175_RS02685

HMPREF0175_RS02680HMPREF0175_RS02680

HMPREF0175_RS02675HMPREF0175_RS02675

5HMPREF0175_RS02670HMPREF0175_RS02670

6HMPREF0175_RS02665HMPREF0175_RS02665

HMPREF0175_RS02660HMPREF0175_RS02660

HMPREF0175_RS02655HMPREF0175_RS02655

HMPREF0175_RS02650HMPREF0175_RS02650

HMPREF0175_RS02645HMPREF0175_RS02645

HMPREF0175_RS02640miaB

Neighborhood gene cards

11 genes in the current genome window.

HMPREF0175_RS02690HMPREF0175_RS02690

Outside P2CS

139 479-139 841 nt · 363 nt · Forward (+)

type II toxin-antitoxin system RelB/DinJ family antitoxin

Protein WP_008783109.1

HMPREF0175_RS02685HMPREF0175_RS02685

Outside P2CS

139 841-140 332 nt · 492 nt · Forward (+)

PIN domain-containing protein

Protein WP_007054468.1

HMPREF0175_RS02680HMPREF0175_RS02680

Outside P2CS

140 394-142 499 nt · 2 106 nt · Reverse (-)

GmrSD restriction endonuclease domain-containing protein

Protein WP_032747025.1

HMPREF0175_RS02675HMPREF0175_RS02675

Outside P2CS

142 589-143 230 nt · 642 nt · Reverse (-)

GNAT family N-acetyltransferase

Protein WP_007052627.1

HMPREF0175_RS02670HMPREF0175_RS02670

RRNarL

143 270-143 995 nt · 726 nt · Reverse (-)

response regulator transcription factor

Protein WP_007056206.1Response regulator NarL family

HMPREF0175_RS02665HMPREF0175_RS02665

HKClassicCurrent focus

144 030-145 262 nt · 1 233 nt · Reverse (-)

sensor histidine kinase

Protein WP_007054471.1Histidine kinase, Classic

HMPREF0175_RS02660HMPREF0175_RS02660

Outside P2CS

145 597-146 442 nt · 846 nt · Forward (+)

DUF5067 domain-containing protein

Protein WP_007057205.1

HMPREF0175_RS02655HMPREF0175_RS02655

Outside P2CS

146 623-147 522 nt · 900 nt · Forward (+)

Bax inhibitor-1/YccA family protein

Protein WP_007052631.1

HMPREF0175_RS02650HMPREF0175_RS02650

Outside P2CS

147 662-148 678 nt · 1 017 nt · Forward (+)

DMT family transporter

Protein WP_007052632.1

HMPREF0175_RS02645HMPREF0175_RS02645

Outside P2CS

148 711-149 451 nt · 741 nt · Reverse (-)

GTP pyrophosphokinase

Protein WP_007056209.1

HMPREF0175_RS02640miaB

Outside P2CS

149 583-151 037 nt · 1 455 nt · Forward (+)

tRNA (N6-isopentenyl adenosine(37)-C2)-methylthiotransferase MiaB

Protein WP_007052635.1

3D Structure

No local structure root: /mnt/p2cs-s3/P2CS_WEB/DATAS/SP_CIF

No local CIF or PDB file was detected for this record.

No CIF or PDB file was found for HKOC_2354145 under /home/biam/MYTOOLS/p2cs-web/DATAS/MassiveFold/work/recovered_by_cluster_all_ranked/clusters.

No UniProt accession is available for this gene.

Clusters

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

Available memberships1 cluster

HKOC_2354145HK

Run 66 sequencesid 100%cov 80%

PFAM HisKA_3

Current gene is the representative sequence.

Selected clusterHKOC_2354145Run 6 · HK · 6 sequences

Representative sequenceGCF_000003135#HMPREF0175_RS02665The 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_2354145

Simplified PFAM architecture for HKOC_2354145

PFAM domain coverage: 69 / 410 aa (16.8%)

1 aa410 aa

HisKA_3

Simplified architecture: HisKA_3
Raw architecture: HisKA_3[200-268]
Domain count: 1
Matched identifier: HKOC_2354145
Positioned domains: HisKA_3 200-268

Cluster members and taxonomy

Representative gene: GCF_000003135#HMPREF0175_RS02665

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

Genome taxonomy

Bifidobacterium longum subsp. longum ATCC 55813

Taxonomy recordBifidobacterium longum subsp. longum ATCC 55813Taxon ID 548 480 · GCF_000003135

AssemblyASM313v1 · Scaffoldhaploid

Genome composition2 396 359 bp · 60,5% GCGenome size and GC content from the linked genome record.

Signal transduction countsGenes 20 · HK 10 · RR 10CheA 0 · PP 0

Ranked taxonomy7 ranked levels available

SuperkingdomBacteriaKingdomBacillatiPhylumActinomycetotaClassActinomycetesOrderBifidobacterialesFamilyBifidobacteriaceaeGenusBifidobacterium

Lineage path1 lineage nodes

1Unknown

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

Related genes

Preview from the same derived genome key