Gene detail

DXB70_RS03095

Response regulator, RpfG family

Clostridium sp. OM05-5BH · GCF_003481505

Open genome Open selected cluster RefSeq

ClassRRTypeRpfGLength704 aaTM0ValidatedNoCompleteYesContextorphan

Gene IDGCF_003481505#DXB70_RS03095Stable P2CS identifier used across views.

GenomeGCF_003481505Bacteria; Bacillati; Bacillota; Clostridia; Eubacteriales; Clostridiaceae; Clostridium

Selected clusterRROC_0029015Run 7 · 1 sequences · id 100% · cov 80% · representative

External referencesWP_347559581.1 · MIST4 DXB70_RS03095RefSeq · MIST4

Domain signature

Compact overview inferred from the domain field

GGDEFResponse_regHD

Protein length704 aaLength used to scale native and Biotite-like views.

Annotated domains33 with usable coordinates.

Domain coverage357 / 704 aa (50.7%)Merged over positioned domains only.

Domain description1 GGDEF,1 Response_reg,1 HDSummary 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 aa704 aa

Domain-by-domain annotation3 items

1 GGDEF#1

138-276 aa · 139 aa · 19.7% of protein

Raw tokenGGDEF:138:5.38e-39:276:151:160

2 Response_reg#2

308-420 aa · 113 aa · 16.1% of protein

Raw tokenResponse_reg:308:2.97e-25:420:114:111

3 HD#3

497-601 aa · 105 aa · 14.9% of protein

Raw tokenHD:497:0.000000000000988:601:105:110

Raw architecture: GGDEF:138:5.38e-39:276:151:160#Response_reg:308:2.97e-25:420:114:111#HD:497:0.000000000000988:601:105:110
Domain description: 1 GGDEF,1 Response_reg,1 HD
TM description: N/A
TMPRED source: No TMPRED file loaded
TMPRED segments: N/A
Complete: Yes

Context mapping

Resolved via p2cs_tcs_context.db when a locus tag match exists

Context labelorphanGCF_003481505::NZ_QULJ01000002.1::G00015

Group size11 locus tag listed below.

HK / RR0 / 1Counts resolved for the local TCS neighborhood.

Context span130312-132426Genomic interval covered by the local TCS group.

Identifiers

Old locus tagDXB70_03095RefSeq proteinWP_347559581.1

Context group IDGCF_003481505::NZ_QULJ01000002.1::G00015

Context members

DXB70_RS03095

Partner locus tags

DXB70_RS03095

Partner old locus tags

DXB70_03095

Partner protein IDs

WP_347559581.1

External references

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

No UniProt / GO / PubMed mapping was found for WP_347559581.1.

Genomic coordinates

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

Current locus tagDXB70_RS03095Primary locus identifier stored in the genes table.

Old locus tagDXB70_03095Legacy locus tag recovered from the local context mapping.

Contig / repliconNZ_QULJ01000002.1Sequence record reported by the local genomic context database.

Genomic interval130 312-132 426 nt2 115 nt · Forward (+)

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

Local TCS group span130 312-132 426 ntGCF_003481505::NZ_QULJ01000002.1::G00015

Quick actions

Open genome Search genes in genome

Local neighborhood

Graphical neighborhood resolved from the local TCS context group on the current contig

GCF_003481505::NZ_QULJ01000002.1::G00015

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.

Context labelorphanNeighborhood members are ordered by genomic coordinates.

Contig / repliconNZ_QULJ01000002.1All displayed genes belong to this local TCS context.

Neighborhood span130 312-132 426 nt2 115 nt

Members11 current focus gene

Local TCS group mapArrow direction follows strand. The current gene is highlighted with a stronger outline.

130 312 nt132 426 nt

+-DXB70_RS03095

Neighborhood gene cards

1 gene in the current local neighborhood.

DXB70_RS03095GCF_003481505#DXB70_RS03095

RRRpfGCurrent focus

130 312-132 426 nt · Forward (+)

Old locus DXB70_03095RefSeq WP_347559581.1

Open current gene

Clusters

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

Available memberships1 cluster

RROC_0029015RR

Run 71 sequencesid 100%cov 80%

PFAM GGDEF + Response_reg + HD_5

Current gene is the representative sequence.

Selected clusterRROC_0029015Run 7 · RR · 1 sequences

Representative sequenceGCF_003481505#DXB70_RS03095The current gene is the representative for this cluster.

PFAM architectureGGDEF + Response_reg + HD_53 domains in the representative PFAM annotation.

Open in cluster search

PFAM architecture for RROC_0029015

Simplified PFAM architecture for RROC_0029015

PFAM domain coverage: 387 / 704 aa (55.0%)

1 aa704 aa

GGDEFResponse_regHD_5

Simplified architecture: GGDEF + Response_reg + HD_5
Raw architecture: GGDEF[137-279] | Response_reg[308-420] | HD_5[490-620]
Domain count: 3
Matched identifier: RROC_0029015
Positioned domains: GGDEF 137-279 ; GGDEF 137-279 ; Response_reg 308-420 ; Response_reg 308-420 ; HD_5 490-620 ; HD_5 490-620

Cluster members and taxonomy

Representative gene: GCF_003481505#DXB70_RS03095

Sankey plot built from the taxonomy of all members in the selected cluster.

Genome taxonomy

Unknown

Taxonomy recordUnknownTaxon ID 2 293 043 · GCF_003481505

AssemblyASM348150v1 · Scaffoldhaploid

Genome composition3 036 263 bp · 48,5% GCClostridium sp. OM05-5BH

Signal transduction countsGenes 58 · HK 30 · RR 25CheA 0 · PP 3

Ranked taxonomy7 ranked levels available

SuperkingdomBacteriaKingdomBacillatiPhylumBacillotaClassClostridiaOrderEubacterialesFamilyClostridiaceaeGenusClostridium

Lineage path7 lineage nodes

1Bacteria2Bacillati3Bacillota4Clostridia5Eubacteriales6Clostridiaceae7Clostridium

Open genome Search genes in genome Search RR genes NCBI assembly files

Related genes

Preview from the same derived genome key