Gene detail

HMPREF0175_RS00700

Response regulator OmpR family

Bifidobacterium longum subsp. longum ATCC 55813 · GCF_000003135

Open genome Open selected cluster RefSeq UniProt

ClassRRTypeOmpRLength234 aaTM0ValidatedNoCompleteYesContextpaired

Gene IDGCF_000003135#HMPREF0175_RS00700Stable P2CS identifier used across views.

GenomeGCF_000003135Unknown

Selected clusterRROC_1047050Run 7 · 44 sequences · id 100% · cov 80% · representative

External referencesWP_032747128.1 · A0AAW4NHH6 · MIST4 HMPREF0175_RS00700RefSeq · UniProt · MIST4

Domain signature

Compact overview inferred from the domain field

Response_regTrans_reg_C

Protein length234 aaLength used to scale native and Biotite-like views.

Annotated domains22 with usable coordinates.

Domain coverage187 / 234 aa (79.9%)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 aa234 aa

Domain-by-domain annotation2 items

1 Response_reg#1

4-113 aa · 110 aa · 47.0% of protein

Raw tokenResponse_reg:4:3.82e-38:113:111:111

2 Trans_reg_C#2

153-229 aa · 77 aa · 32.9% of protein

Raw tokenTrans_reg_C:153:1.39e-33:229:77:77

Raw architecture: Response_reg:4:3.82e-38:113:111:111#Trans_reg_C:153:1.39e-33:229:77:77
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_GG666856.1::G00010

Group size22 locus tags listed below.

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

Context span241142-243376Genomic interval covered by the local TCS group.

Identifiers

Old locus tagHMPREF0175_0217RefSeq proteinWP_032747128.1

Context group IDGCF_000003135::NZ_GG666856.1::G00010

Context members

HMPREF0175_RS00705HMPREF0175_RS00700

Partner locus tags

HMPREF0175_RS00705HMPREF0175_RS00700

Partner old locus tags

HMPREF0175_0216HMPREF0175_0217

Partner protein IDs

WP_007054795.1 WP_032747128.1

External references

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

RefSeqWP_032747128.1Primary protein accession used for annex mappings.

UniProt accessionA0AAW4NHH6Primary UniProt accession resolved in the annex database.

UniProt IDA0AAW4NHH6_BIFLNDisplay identifier provided by UniProt.

GO / PubMed5 / 0Unique 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

Genomic coordinates

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

Current locus tagHMPREF0175_RS00700Primary locus identifier stored in the genes table.

Old locus tagHMPREF0175_0217Legacy locus tag recovered from the local context mapping.

Contig / repliconNZ_GG666856.1Sequence record reported by the local genomic context database.

Genomic interval242 672-243 376 nt705 nt · Forward (+)

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

Local TCS group span241 142-243 376 ntGCF_000003135::NZ_GG666856.1::G00010

Quick actions

Open genome Search genes in genome

Genome neighborhood

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

GCF_000003135 · NZ_GG666856.1

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_RS0070011 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_RS00725HMPREF0175_RS00725

HMPREF0175_RS00720HMPREF0175_RS00720

HMPREF0175_RS00715HMPREF0175_RS00715

HMPREF0175_RS00710mtnN

5HMPREF0175_RS00705HMPREF0175_RS00705

6HMPREF0175_RS00700HMPREF0175_RS00700

HMPREF0175_RS00695pstS

HMPREF0175_RS00690pstC

HMPREF0175_RS00685pstA

HMPREF0175_RS00680pstB

HMPREF0175_RS00675HMPREF0175_RS00675

Neighborhood gene cards

11 genes in the current genome window.

HMPREF0175_RS00725HMPREF0175_RS00725

Outside P2CS

235 927-237 270 nt · 1 344 nt · Forward (+)

C1 family peptidase

Protein WP_007051443.1

HMPREF0175_RS00720HMPREF0175_RS00720

Outside P2CS

237 562-238 695 nt · 1 134 nt · Forward (+)

3-deoxy-7-phosphoheptulonate synthase

Protein WP_007051442.1

HMPREF0175_RS00715HMPREF0175_RS00715

Outside P2CS

238 824-240 056 nt · 1 233 nt · Forward (+)

3-deoxy-7-phosphoheptulonate synthase

Protein WP_007051440.1

HMPREF0175_RS00710mtnN

Outside P2CS

240 178-240 891 nt · 714 nt · Forward (+)

5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase

Protein WP_007051439.1

HMPREF0175_RS00705HMPREF0175_RS00705

HKClassic

241 142-242 473 nt · 1 332 nt · Forward (+)

sensor histidine kinase

Protein WP_007054795.1Histidine kinase, Classic

HMPREF0175_RS00700HMPREF0175_RS00700

RROmpRCurrent focus

242 672-243 376 nt · 705 nt · Forward (+)

response regulator transcription factor

Protein WP_032747128.1Response regulator OmpR family

HMPREF0175_RS00695pstS

Outside P2CS

243 625-244 758 nt · 1 134 nt · Forward (+)

phosphate ABC transporter substrate-binding protein PstS

Protein WP_007051436.1

HMPREF0175_RS00690pstC

Outside P2CS

244 969-245 922 nt · 954 nt · Forward (+)

phosphate ABC transporter permease subunit PstC

Protein WP_007055708.1

HMPREF0175_RS00685pstA

Outside P2CS

245 922-246 920 nt · 999 nt · Forward (+)

phosphate ABC transporter permease PstA

Protein WP_007054798.1

HMPREF0175_RS00680pstB

Outside P2CS

246 973-247 752 nt · 780 nt · Forward (+)

phosphate ABC transporter ATP-binding protein PstB

Protein WP_007054799.1

HMPREF0175_RS00675HMPREF0175_RS00675

Outside P2CS

248 047-248 625 nt · 579 nt · Forward (+)

LemA family protein

Protein WP_007054801.1

3D Structure

Clusters

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

Available memberships1 cluster

RROC_1047050RR

Run 744 sequencesid 100%cov 80%

PFAM Response_reg + Trans_reg_C

Current gene is the representative sequence.

Selected clusterRROC_1047050Run 7 · RR · 44 sequences

Representative sequenceGCF_000003135#HMPREF0175_RS00700The 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_1047050

Simplified PFAM architecture for RROC_1047050

PFAM domain coverage: 183 / 234 aa (78.2%)

1 aa234 aa

Response_regTrans_reg_C

Simplified architecture: Response_reg + Trans_reg_C
Raw architecture: Response_reg[4-113] | Trans_reg_C[156-228]
Domain count: 2
Matched identifier: RROC_1047050
Positioned domains: Response_reg 4-113 ; Response_reg 4-113 ; Trans_reg_C 156-228 ; Trans_reg_C 156-228

Cluster members and taxonomy

Representative gene: GCF_000003135#HMPREF0175_RS00700

Loading taxonomy Sankey…

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