Gene detail

HMPREF0175_RS09160

Response regulator NarL family

Bifidobacterium longum subsp. longum ATCC 55813 · GCF_000003135

Open genome Open selected cluster RefSeq UniProt

ClassRRTypeNarLLength217 aaTM0ValidatedNoCompleteYesContextpaired

Gene IDGCF_000003135#HMPREF0175_RS09160Stable P2CS identifier used across views.

GenomeGCF_000003135Unknown

Selected clusterRROC_1847431Run 7 · 553 sequences · id 100% · cov 80% · representative

External referencesWP_007052109.1 · A0AAV3FML7 · MIST4 HMPREF0175_RS09160RefSeq · UniProt · MIST4

Domain signature

Compact overview inferred from the domain field

Response_regHTH_LUXR

Protein length217 aaLength used to scale native and Biotite-like views.

Annotated domains22 with usable coordinates.

Domain coverage158 / 217 aa (72.8%)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 aa217 aa

Domain-by-domain annotation2 items

1 Response_reg#1

3-106 aa · 104 aa · 47.9% of protein

Raw tokenResponse_reg:3:2.25e-21:106:104:111

2 HTH_LUXR#2

158-211 aa · 54 aa · 24.9% of protein

Raw tokenHTH_LUXR:158:2.04e-20:211:54:58

Raw architecture: Response_reg:3:2.25e-21:106:104:111#HTH_LUXR:158:2.04e-20:211:54:58
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::G00001

Group size22 locus tags listed below.

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

Context span96963-98968Genomic interval covered by the local TCS group.

Identifiers

Old locus tagHMPREF0175_0381RefSeq proteinWP_007052109.1

Context group IDGCF_000003135::NZ_GG666849.1::G00001

Context members

HMPREF0175_RS09165HMPREF0175_RS09160

Partner locus tags

HMPREF0175_RS09165HMPREF0175_RS09160

Partner old locus tags

HMPREF0175_0380HMPREF0175_0381

Partner protein IDs

WP_007053402.1 WP_007052109.1

External references

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

RefSeqWP_007052109.1Primary protein accession used for annex mappings.

UniProt accessionA0AAV3FML7Primary UniProt accession resolved in the annex database.

UniProt IDA0AAV3FML7_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

23682142

Genomic coordinates

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

Current locus tagHMPREF0175_RS09160Primary locus identifier stored in the genes table.

Old locus tagHMPREF0175_0381Legacy locus tag recovered from the local context mapping.

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

Genomic interval98 315-98 968 nt654 nt · Forward (+)

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

Local TCS group span96 963-98 968 ntGCF_000003135::NZ_GG666849.1::G00001

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_RS0916011 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_RS09185HMPREF0175_RS09185

HMPREF0175_RS09180HMPREF0175_RS09180

HMPREF0175_RS09175HMPREF0175_RS09175

HMPREF0175_RS09170HMPREF0175_RS09170

5HMPREF0175_RS09165HMPREF0175_RS09165

6HMPREF0175_RS09160HMPREF0175_RS09160

HMPREF0175_RS09155HMPREF0175_RS09155

HMPREF0175_RS09150HMPREF0175_RS09150

HMPREF0175_RS09145HMPREF0175_RS09145

HMPREF0175_RS09140HMPREF0175_RS09140

HMPREF0175_RS09135HMPREF0175_RS09135

Neighborhood gene cards

11 genes in the current genome window.

HMPREF0175_RS09185HMPREF0175_RS09185

Outside P2CS

91 373-92 851 nt · 1 479 nt · Forward (+)

ATP-binding protein

Protein WP_007052115.1

HMPREF0175_RS09180HMPREF0175_RS09180

Outside P2CS

92 856-94 268 nt · 1 413 nt · Reverse (-)

ABC transporter permease

Protein WP_007052114.1

HMPREF0175_RS09175HMPREF0175_RS09175

Outside P2CS

94 255-95 493 nt · 1 239 nt · Reverse (-)

ABC transporter permease

Protein WP_007052113.1

HMPREF0175_RS09170HMPREF0175_RS09170

Outside P2CS

95 594-96 577 nt · 984 nt · Reverse (-)

ABC transporter ATP-binding protein

Protein WP_007057287.1

HMPREF0175_RS09165HMPREF0175_RS09165

HKClassic

96 963-98 315 nt · 1 353 nt · Forward (+)

sensor histidine kinase

Protein WP_007053402.1Histidine kinase, Classic

HMPREF0175_RS09160HMPREF0175_RS09160

RRNarLCurrent focus

98 315-98 968 nt · 654 nt · Forward (+)

response regulator transcription factor

Protein WP_007052109.1Response regulator NarL family

HMPREF0175_RS09155HMPREF0175_RS09155

Outside P2CS

99 152-99 775 nt · 624 nt · Reverse (-)

DUF47 domain-containing protein

Protein WP_007052108.1

HMPREF0175_RS09150HMPREF0175_RS09150

Outside P2CS

99 793-100 845 nt · 1 053 nt · Reverse (-)

inorganic phosphate transporter

Protein WP_007052107.1

HMPREF0175_RS09145HMPREF0175_RS09145

Outside P2CS

100 965-101 162 nt · 198 nt · Reverse (-)

YbdD/YjiX family protein

Protein WP_007052106.1

HMPREF0175_RS09140HMPREF0175_RS09140

Outside P2CS

101 220-103 619 nt · 2 400 nt · Reverse (-)

carbon starvation CstA family protein

Protein WP_007052105.1

HMPREF0175_RS09135HMPREF0175_RS09135

Outside P2CS

103 864-105 159 nt · 1 296 nt · Forward (+)

alpha-amylase family protein

Protein WP_032746753.1

3D Structure

UniProt CIF structure root: /mnt/p2cs-s3/P2CS_WEB/DATAS/SP_CIF

Loading 3D structure...

Response_reg3-106 aa

HTH_LUXR158-211 aa

Structure domain maps

The initial PFAM_pred3D-style renderer is shown by default, using domain positions stored in P2CS for this gene. The optional Biotite-like renderer can be enabled from config.ini.

GCF_000003135#HMPREF0175_RS09160

Initial PFAM_pred3D-style view.

No CIF or PDB file was found for RROC_1847431 under /home/biam/MYTOOLS/p2cs-web/DATAS/MassiveFold/work/recovered_by_cluster_all_ranked/clusters.

Using the UniProt CIF structure for A0AAV3FML7.

Clusters

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

Available memberships1 cluster

RROC_1847431RR

Run 7553 sequencesid 100%cov 80%

PFAM Response_reg + GerE

Current gene is the representative sequence.

Selected clusterRROC_1847431Run 7 · RR · 553 sequences

Representative sequenceGCF_000003135#HMPREF0175_RS09160The 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_1847431

Simplified PFAM architecture for RROC_1847431

PFAM domain coverage: 158 / 217 aa (72.8%)

1 aa217 aa

Response_regGerE

Simplified architecture: Response_reg + GerE
Raw architecture: Response_reg[3-107] | GerE[158-210]
Domain count: 2
Matched identifier: RROC_1847431
Positioned domains: Response_reg 3-107 ; Response_reg 3-107 ; GerE 158-210 ; GerE 158-210

Cluster members and taxonomy

Representative gene: GCF_000003135#HMPREF0175_RS09160

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 RR genes NCBI assembly files

Related genes

Preview from the same derived genome key