Gene detail

HMPREF0175_RS08255

Response regulator OmpR family

Bifidobacterium longum subsp. longum ATCC 55813 · GCF_000003135

Open genome Open selected cluster RefSeq UniProt

ClassRRTypeOmpRLength240 aaTM0ValidatedNoCompleteYesContextpaired

Gene IDGCF_000003135#HMPREF0175_RS08255Stable P2CS identifier used across views.

GenomeGCF_000003135Unknown

Selected clusterRROC_0881917Run 7 · 640 sequences · id 100% · cov 80% · representative

External referencesWP_007051909.1 · D6ZTH4 · MIST4 HMPREF0175_RS08255RefSeq · UniProt · MIST4

Domain signature

Compact overview inferred from the domain field

Response_regTrans_reg_C

Protein length240 aaLength used to scale native and Biotite-like views.

Annotated domains22 with usable coordinates.

Domain coverage180 / 240 aa (75.0%)Merged over positioned domains only.

Domain description1 Response_reg,1 Trans_reg_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 aa240 aa

Domain-by-domain annotation2 items

1 Response_reg#1

15-122 aa · 108 aa · 45.0% of protein

Raw tokenResponse_reg:15:3.61e-36:122:109:111

2 Trans_reg_C#2

164-235 aa · 72 aa · 30.0% of protein

Raw tokenTrans_reg_C:164:1.73e-30:235:77:77

Raw architecture: Response_reg:15:3.61e-36:122:109:111#Trans_reg_C:164:1.73e-30:235:77:77
Domain description: 1 Response_reg,1 Trans_reg_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_GG666849.1::G00004

Group size22 locus tags listed below.

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

Context span328921-330716Genomic interval covered by the local TCS group.

Identifiers

Old locus tagHMPREF0175_0589RefSeq proteinWP_007051909.1

Context group IDGCF_000003135::NZ_GG666849.1::G00004

Context members

HMPREF0175_RS08255HMPREF0175_RS08250

Partner locus tags

HMPREF0175_RS08255HMPREF0175_RS08250

Partner old locus tags

HMPREF0175_0589HMPREF0175_0590

Partner protein IDs

WP_007051909.1 WP_007053568.1

External references

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

RefSeqWP_007051909.1Primary protein accession used for annex mappings.

UniProt accessionD6ZTH4Primary UniProt accession resolved in the annex database.

UniProt IDD6ZTH4_BIFLJDisplay identifier provided by UniProt.

GO / PubMed5 / 1Unique GO terms and literature references available below.

Reference hubs

Open RefSeq Open UniProt accession

GO terms

GO:0005829 GO:0032993 GO:0000156 GO:0000976 GO:0006355

PubMed

20525832

Genomic coordinates

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

Current locus tagHMPREF0175_RS08255Primary locus identifier stored in the genes table.

Old locus tagHMPREF0175_0589Legacy locus tag recovered from the local context mapping.

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

Genomic interval328 921-329 643 nt723 nt · Forward (+)

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

Local TCS group span328 921-330 716 ntGCF_000003135::NZ_GG666849.1::G00004

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_RS0825511 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_RS08280HMPREF0175_RS08280

HMPREF0175_RS08275HMPREF0175_RS08275

HMPREF0175_RS08270ispF

HMPREF0175_RS08265HMPREF0175_RS08265

HMPREF0175_RS08260glgB

6HMPREF0175_RS08255HMPREF0175_RS08255

7HMPREF0175_RS08250HMPREF0175_RS08250

HMPREF0175_RS08245HMPREF0175_RS08245

HMPREF0175_RS08240HMPREF0175_RS08240

HMPREF0175_RS08235HMPREF0175_RS08235

HMPREF0175_RS08230HMPREF0175_RS08230

Neighborhood gene cards

11 genes in the current genome window.

HMPREF0175_RS08280HMPREF0175_RS08280

Outside P2CS

323 387-324 277 nt · 891 nt · Forward (+)

ABC transporter ATP-binding protein

Protein WP_007053564.1

HMPREF0175_RS08275HMPREF0175_RS08275

Outside P2CS

324 344-325 177 nt · 834 nt · Forward (+)

metal ABC transporter permease

Protein WP_007051913.1

HMPREF0175_RS08270ispF

Outside P2CS

325 229-325 753 nt · 525 nt · Reverse (-)

2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase

Protein WP_007053565.1

HMPREF0175_RS08265HMPREF0175_RS08265

Outside P2CS

325 862-326 455 nt · 594 nt · Reverse (-)

CarD family transcriptional regulator

Protein WP_007053566.1

HMPREF0175_RS08260glgB

Outside P2CS

326 633-328 885 nt · 2 253 nt · Forward (+)

1,4-alpha-glucan branching protein GlgB

Protein WP_007053567.1

HMPREF0175_RS08255HMPREF0175_RS08255

RROmpRCurrent focus

328 921-329 643 nt · 723 nt · Forward (+)

response regulator transcription factor

Protein WP_007051909.1Response regulator OmpR family

HMPREF0175_RS08250HMPREF0175_RS08250

HKClassic

329 643-330 716 nt · 1 074 nt · Forward (+)

sensor histidine kinase

Protein WP_007053568.1Histidine kinase, Classic

HMPREF0175_RS08245HMPREF0175_RS08245

Outside P2CS

330 784-331 170 nt · 387 nt · Forward (+)

LexA family protein

Protein WP_007051907.1

HMPREF0175_RS08240HMPREF0175_RS08240

Outside P2CS

331 086-331 808 nt · 723 nt · Reverse (-)

ComF family protein

Protein WP_007051906.1

HMPREF0175_RS08235HMPREF0175_RS08235

Outside P2CS

331 818-332 624 nt · 807 nt · Reverse (-)

HAD-IIB family hydrolase

Protein WP_007053569.1

HMPREF0175_RS08230HMPREF0175_RS08230

Outside P2CS

332 779-333 141 nt · 363 nt · Forward (+)

metallopeptidase family protein

Protein WP_007053570.1

3D Structure

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

Loading 3D structure...

Response_reg15-122 aa

Trans_reg_C164-235 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_RS08255

Initial PFAM_pred3D-style view.

No CIF or PDB file was found for RROC_0881917 under /home/biam/MYTOOLS/p2cs-web/DATAS/MassiveFold/work/recovered_by_cluster_all_ranked/clusters.

Using the UniProt CIF structure for D6ZTH4.

Clusters

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

Available memberships1 cluster

RROC_0881917RR

Run 7640 sequencesid 100%cov 80%

PFAM Response_reg + Trans_reg_C

Current gene is the representative sequence.

Selected clusterRROC_0881917Run 7 · RR · 640 sequences

Representative sequenceGCF_000003135#HMPREF0175_RS08255The current gene is the representative for this cluster.

PFAM architectureResponse_reg + Trans_reg_C2 domains in the representative PFAM annotation.

Open in cluster search

PFAM architecture for RROC_0881917

Simplified PFAM architecture for RROC_0881917

PFAM domain coverage: 180 / 240 aa (75.0%)

1 aa240 aa

Response_regTrans_reg_C

Simplified architecture: Response_reg + Trans_reg_C
Raw architecture: Response_reg[15-122] | Trans_reg_C[164-235]
Domain count: 2
Matched identifier: RROC_0881917
Positioned domains: Response_reg 15-122 ; Response_reg 15-122 ; Trans_reg_C 164-235 ; Trans_reg_C 164-235

Cluster members and taxonomy

Representative gene: GCF_000003135#HMPREF0175_RS08255

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