Gene detail

HMPREF0175_RS06465

Probable incomplete histidine kinase

Bifidobacterium longum subsp. longum ATCC 55813 · GCF_000003135

Open genome Open selected cluster

ClassHKTypeClassicLength427 aaTM0ValidatedNoCompleteNoContextNo local context

Gene IDGCF_000003135#HMPREF0175_RS06465Stable P2CS identifier used across views.

GenomeGCF_000003135Unknown

Selected clusterIHKOC_095112Run 0 · 300 sequences · id 100% · cov 80%

External referencesMIST4 HMPREF0175_RS06465MIST4

Domain signature

Compact overview inferred from the domain field

HATPase_c

Protein length427 aaLength used to scale native and Biotite-like views.

Annotated domains11 with usable coordinates.

Domain coverage81 / 427 aa (19.0%)Merged over positioned domains only.

Domain description1 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 aa427 aa

Domain-by-domain annotation1 item

1 HATPase_c#1

338-418 aa · 81 aa · 19.0% of protein

Raw tokenHATPase_c:338:0.000000471:418:96:109

Raw architecture: HATPase_c:338:0.000000471:418:96:109
Domain description: 1 HATPase_c
TM description: N/A
TMPRED source: No TMPRED file loaded
TMPRED segments: N/A
Complete: No

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

No local TCS context mapping is available for this gene.

External references

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

No external UniProt / GO / PubMed mapping is available for this gene.

Genomic coordinates

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

Current locus tagHMPREF0175_RS06465Primary locus identifier stored in the genes table.

Old locus tagUnavailableNo previous locus tag available for this gene.

Contig / repliconUnavailableNo contig or replicon mapping is available for this gene.

Genomic intervalUnavailableNo start/end genomic coordinates are available for this gene.

StrandUnavailableStrand sign follows the local context database convention.

Local TCS group spanUnavailableNo grouped neighborhood span is available for this gene.

Quick actions

Open genome Search genes in genome

Genome neighborhood

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

GCF_000003135 · NZ_GG666850.1

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_RS0646511 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_RS06490gnpA

HMPREF0175_RS06485nahK

HMPREF0175_RS06480HMPREF0175_RS06480

HMPREF0175_RS06475galE

5HMPREF0175_RS06470HMPREF0175_RS06470

6HMPREF0175_RS06465HMPREF0175_RS06465

HMPREF0175_RS12120HMPREF0175_RS12120

HMPREF0175_RS06455HMPREF0175_RS06455

HMPREF0175_RS06450HMPREF0175_RS06450

HMPREF0175_RS06445HMPREF0175_RS06445

HMPREF0175_RS06440HMPREF0175_RS06440

Neighborhood gene cards

11 genes in the current genome window.

HMPREF0175_RS06490gnpA

Outside P2CS

137 136-139 391 nt · 2 256 nt · Forward (+)

1,3-beta-galactosyl-N-acetylhexosamine phosphorylase

Protein WP_007053830.1

HMPREF0175_RS06485nahK

Outside P2CS

139 419-140 498 nt · 1 080 nt · Forward (+)

N-acetylhexosamine 1-kinase

Protein WP_007053831.1

HMPREF0175_RS06480HMPREF0175_RS06480

Outside P2CS

140 545-142 092 nt · 1 548 nt · Forward (+)

UDP-glucose--hexose-1-phosphate uridylyltransferase

Protein WP_007053832.1

HMPREF0175_RS06475galE

Outside P2CS

142 162-143 184 nt · 1 023 nt · Forward (+)

UDP-glucose 4-epimerase GalE

Protein WP_007052336.1

HMPREF0175_RS06470HMPREF0175_RS06470

RRNarL

143 232-143 927 nt · 696 nt · Reverse (-)

LuxR C-terminal-related transcriptional regulator

Protein WP_007053833.1Response regulator NarL family

HMPREF0175_RS06465HMPREF0175_RS06465

HKClassicCurrent focus

143 924-145 207 nt · 1 284 nt · Reverse (-)

ATP-binding protein

Protein WP_007052338.1Probable incomplete histidine kinase

HMPREF0175_RS12120HMPREF0175_RS12120

Outside P2CS

145 321-147 066 nt · 1 746 nt · Forward (+)

PspC domain-containing protein

Protein WP_175282295.1

HMPREF0175_RS06455HMPREF0175_RS06455

Outside P2CS

147 096-147 803 nt · 708 nt · Forward (+)

hypothetical protein

Protein WP_013582916.1

HMPREF0175_RS06450HMPREF0175_RS06450

Outside P2CS

147 908-149 509 nt · 1 602 nt · Forward (+)

alpha/beta hydrolase family protein

Protein WP_007053836.1

HMPREF0175_RS06445HMPREF0175_RS06445

Outside P2CS

149 659-150 291 nt · 633 nt · Reverse (-)

DUF4125 family protein

Protein WP_007053837.1

HMPREF0175_RS06440HMPREF0175_RS06440

Outside P2CS

150 367-152 730 nt · 2 364 nt · Reverse (-)

DUF4037 domain-containing protein

Protein WP_007052343.1

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 IHKOC_095112 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

IHKOC_095112IHK

IHKOC clustering300 sequencesid 100%cov 80%

Representative GCF_003471355#DW237_RS01370

Selected clusterIHKOC_095112IHKOC clustering · IHK · 300 sequences

Representative sequenceGCF_003471355#DW237_RS01370Use this link to inspect the representative gene detail.

PFAM architectureNo PFAM architecture available0 domain in the representative PFAM annotation.

Open in cluster search Open representative gene

PFAM architecture for IHKOC_095112

Simplified PFAM architecture for IHKOC_095112

PFAM domain coverage: 0 / 427 aa (0.0%)

Simplified architecture: N/A
Domain count: 0
Matched identifier: IHKOC_095112

Cluster members and taxonomy

Representative gene: GCF_003471355#DW237_RS01370

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