Gene detail

HMPREF0175_RS09025

Response regulator NarL family

Bifidobacterium longum subsp. longum ATCC 55813 · GCF_000003135

Open genome Open selected cluster RefSeq UniProt

ClassRRTypeNarLLength296 aaTM0ValidatedNoCompleteYesContextpaired

Gene IDGCF_000003135#HMPREF0175_RS09025Stable P2CS identifier used across views.

GenomeGCF_000003135Unknown

Selected clusterRROC_0580156Run 7 · 118 sequences · id 100% · cov 80% · representative

External referencesWP_007053424.1 · A0AA46JXS4 · MIST4 HMPREF0175_RS09025RefSeq · UniProt · MIST4

Domain signature

Compact overview inferred from the domain field

Response_regHTH_LUXR

Protein length296 aaLength used to scale native and Biotite-like views.

Annotated domains22 with usable coordinates.

Domain coverage196 / 296 aa (66.2%)Merged over positioned domains only.

Domain description1 Response_reg,1 HTH_LUXRSummary 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 aa296 aa

Domain-by-domain annotation2 items

1 Response_reg#1

9-146 aa · 138 aa · 46.6% of protein

Raw tokenResponse_reg:9:7.61e-27:146:138:111

2 HTH_LUXR#2

233-290 aa · 58 aa · 19.6% of protein

Raw tokenHTH_LUXR:233:5.75e-25:290:58:58

Raw architecture: Response_reg:9:7.61e-27:146:138:111#HTH_LUXR:233:5.75e-25:290:58:58
Domain description: 1 Response_reg,1 HTH_LUXR
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_GG666849.1::G00002

Group size22 locus tags listed below.

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

Context span130162-133533Genomic interval covered by the local TCS group.

Identifiers

Old locus tagHMPREF0175_0411RefSeq proteinWP_007053424.1

Context group IDGCF_000003135::NZ_GG666849.1::G00002

Context members

HMPREF0175_RS09030HMPREF0175_RS09025

Partner locus tags

HMPREF0175_RS09030HMPREF0175_RS09025

Partner old locus tags

HMPREF0175_0410HMPREF0175_0411

Partner protein IDs

WP_007058356.1 WP_007053424.1

External references

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

RefSeqWP_007053424.1Primary protein accession used for annex mappings.

UniProt accessionA0AA46JXS4Primary UniProt accession resolved in the annex database.

UniProt IDA0AA46JXS4_BIFLLDisplay identifier provided by UniProt.

GO / PubMed3 / 1Unique GO terms and literature references available below.

Reference hubs

Open RefSeq Open UniProt accession

GO terms

GO:0003677 GO:0000160 GO:0006355

PubMed

31201276

Genomic coordinates

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

Current locus tagHMPREF0175_RS09025Primary locus identifier stored in the genes table.

Old locus tagHMPREF0175_0411Legacy locus tag recovered from the local context mapping.

Contig / repliconNZ_GG666849.1Sequence record reported by the local genomic context database.

Genomic interval132 643-133 533 nt891 nt · Forward (+)

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

Local TCS group span130 162-133 533 ntGCF_000003135::NZ_GG666849.1::G00002

Quick actions

Open genome Search genes in genome

Genome neighborhood

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

GCF_000003135 · NZ_GG666849.1

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_RS0902511 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_RS11795HMPREF0175_RS11795

HMPREF0175_RS09045ychF

HMPREF0175_RS09040proC

HMPREF0175_RS09035HMPREF0175_RS09035

5HMPREF0175_RS09030HMPREF0175_RS09030

6HMPREF0175_RS09025HMPREF0175_RS09025

HMPREF0175_RS09020HMPREF0175_RS09020

HMPREF0175_RS0109585HMPREF0175_RS0109585

HMPREF0175_RS09015HMPREF0175_RS09015

HMPREF0175_RS09010HMPREF0175_RS09010

HMPREF0175_RS09005HMPREF0175_RS09005

Neighborhood gene cards

11 genes in the current genome window.

HMPREF0175_RS11795HMPREF0175_RS11795

Outside P2CS

125 805-126 005 nt · 201 nt · Forward (+)

hypothetical protein

Protein WP_165506154.1

HMPREF0175_RS09045ychF

Outside P2CS

126 487-127 581 nt · 1 095 nt · Reverse (-)

redox-regulated ATPase YchF

Protein WP_008783009.1

HMPREF0175_RS09040proC

Outside P2CS

127 715-128 536 nt · 822 nt · Reverse (-)

pyrroline-5-carboxylate reductase

Protein WP_007053421.1

HMPREF0175_RS09035HMPREF0175_RS09035

Outside P2CS

128 598-130 076 nt · 1 479 nt · Reverse (-)

alpha/beta fold hydrolase

Protein WP_007053422.1

HMPREF0175_RS09030HMPREF0175_RS09030

HKClassic

130 162-132 621 nt · 2 460 nt · Forward (+)

sensor histidine kinase

Protein WP_007058356.1Histidine kinase, Classic

HMPREF0175_RS09025HMPREF0175_RS09025

RRNarLCurrent focus

132 643-133 533 nt · 891 nt · Forward (+)

response regulator transcription factor

Protein WP_007053424.1Response regulator NarL family

HMPREF0175_RS09020HMPREF0175_RS09020

Outside P2CS

133 566-136 418 nt · 2 853 nt · Reverse (-)

ABC transporter permease

Protein WP_007057200.1

HMPREF0175_RS0109585HMPREF0175_RS0109585

Outside P2CS

136 447-137 361 nt · 915 nt · Reverse (-)

ABC transporter ATP-binding protein

Protein WP_007057199.1

HMPREF0175_RS09015HMPREF0175_RS09015

Outside P2CS

137 710-139 026 nt · 1 317 nt · Reverse (-)

O-acetylhomoserine aminocarboxypropyltransferase/cysteine synthase family protein

Protein WP_007053427.1

HMPREF0175_RS09010HMPREF0175_RS09010

Outside P2CS

139 500-140 372 nt · 873 nt · Forward (+)

pyridoxamine kinase

Protein WP_007053428.1

HMPREF0175_RS09005HMPREF0175_RS09005

Outside P2CS

140 609-141 112 nt · 504 nt · Forward (+)

YraN family protein

Protein WP_007053429.1

3D Structure

Clusters

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

Available memberships1 cluster

RROC_0580156RR

Run 7118 sequencesid 100%cov 80%

PFAM Response_reg + GerE

Current gene is the representative sequence.

Selected clusterRROC_0580156Run 7 · RR · 118 sequences

Representative sequenceGCF_000003135#HMPREF0175_RS09025The current gene is the representative for this cluster.

PFAM architectureResponse_reg + GerE2 domains in the representative PFAM annotation.

Open in cluster search

PFAM architecture for RROC_0580156

Simplified PFAM architecture for RROC_0580156

PFAM domain coverage: 125 / 296 aa (42.2%)

1 aa296 aa

Response_regGerE

Simplified architecture: Response_reg + GerE
Raw architecture: Response_reg[9-77] | GerE[235-290]
Domain count: 2
Matched identifier: RROC_0580156
Positioned domains: Response_reg 9-77 ; Response_reg 9-77 ; GerE 235-290 ; GerE 235-290

Cluster members and taxonomy

Representative gene: GCF_000003135#HMPREF0175_RS09025

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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 RR genes NCBI assembly files

Related genes

Preview from the same derived genome key