Gene detail

DXD06_RS03535

Response regulator, RpfG family

Roseburia sp. TF10-5 · GCF_003462365

Open genome Open selected cluster RefSeq

ClassRRTypeRpfGLength657 aaTM0ValidatedNoCompleteYesContextorphan

Gene IDGCF_003462365#DXD06_RS03535Stable P2CS identifier used across views.

GenomeGCF_003462365Bacteria; Bacillati; Bacillota; Clostridia; Lachnospirales; Lachnospiraceae; Roseburia

Selected clusterRROC_0035296Run 7 · 1 sequences · id 100% · cov 80% · representative

External referencesWP_117830660.1 · MIST4 DXD06_RS03535RefSeq · MIST4

Domain signature

Compact overview inferred from the domain field

GGDEFResponse_regHD

Protein length657 aaLength used to scale native and Biotite-like views.

Annotated domains33 with usable coordinates.

Domain coverage382 / 657 aa (58.1%)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 aa657 aa

Domain-by-domain annotation3 items

1 GGDEF#1

141-284 aa · 144 aa · 21.9% of protein

Raw tokenGGDEF:141:6.4e-38:284:156:160

2 Response_reg#2

311-423 aa · 113 aa · 17.2% of protein

Raw tokenResponse_reg:311:6.69e-26:423:114:111

3 HD#3

480-604 aa · 125 aa · 19.0% of protein

Raw tokenHD:480:0.0000000000000145:604:125:110

Raw architecture: GGDEF:141:6.4e-38:284:156:160#Response_reg:311:6.69e-26:423:114:111#HD:480:0.0000000000000145:604:125:110
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_003462365::NZ_QTYW01000002.1::G00017

Group size11 locus tag listed below.

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

Context span302846-304819Genomic interval covered by the local TCS group.

Identifiers

Old locus tagDXD06_03540RefSeq proteinWP_117830660.1

Context group IDGCF_003462365::NZ_QTYW01000002.1::G00017

Context members

DXD06_RS03535

Partner locus tags

DXD06_RS03535

Partner old locus tags

DXD06_03540

Partner protein IDs

WP_117830660.1

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_117830660.1.

Genomic coordinates

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

Current locus tagDXD06_RS03535Primary locus identifier stored in the genes table.

Old locus tagDXD06_03540Legacy locus tag recovered from the local context mapping.

Contig / repliconNZ_QTYW01000002.1Sequence record reported by the local genomic context database.

Genomic interval302 846-304 819 nt1 974 nt · Reverse (-)

StrandReverse (-)Strand sign follows the local context database convention.

Local TCS group span302 846-304 819 ntGCF_003462365::NZ_QTYW01000002.1::G00017

Quick actions

Open genome Search genes in genome

Local neighborhood

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

GCF_003462365::NZ_QTYW01000002.1::G00017

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_QTYW01000002.1All displayed genes belong to this local TCS context.

Neighborhood span302 846-304 819 nt1 974 nt

Members11 current focus gene

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

302 846 nt304 819 nt

+-DXD06_RS03535

Neighborhood gene cards

1 gene in the current local neighborhood.

DXD06_RS03535GCF_003462365#DXD06_RS03535

RRRpfGCurrent focus

302 846-304 819 nt · Reverse (-)

Old locus DXD06_03540RefSeq WP_117830660.1

Open current gene

Clusters

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

Available memberships1 cluster

RROC_0035296RR

Run 71 sequencesid 100%cov 80%

PFAM GGDEF + Response_reg + HD_5

Current gene is the representative sequence.

Selected clusterRROC_0035296Run 7 · RR · 1 sequences

Representative sequenceGCF_003462365#DXD06_RS03535The 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_0035296

Simplified PFAM architecture for RROC_0035296

PFAM domain coverage: 406 / 657 aa (61.8%)

1 aa657 aa

GGDEFResponse_regHD_5

Simplified architecture: GGDEF + Response_reg + HD_5
Raw architecture: GGDEF[140-283] | Response_reg[311-423] | HD_5[475-623]
Domain count: 3
Matched identifier: RROC_0035296
Positioned domains: GGDEF 140-283 ; GGDEF 140-283 ; Response_reg 311-423 ; Response_reg 311-423 ; HD_5 475-623 ; HD_5 475-623

Cluster members and taxonomy

Representative gene: GCF_003462365#DXD06_RS03535

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

Genome taxonomy

Unknown

Taxonomy recordUnknownTaxon ID 2 293 144 · GCF_003462365

AssemblyASM346236v1 · Scaffoldhaploid

Genome composition3 443 473 bp · 43,0% GCRoseburia sp. TF10-5

Signal transduction countsGenes 112 · HK 50 · RR 61CheA 1 · PP 1

Ranked taxonomy7 ranked levels available

SuperkingdomBacteriaKingdomBacillatiPhylumBacillotaClassClostridiaOrderLachnospiralesFamilyLachnospiraceaeGenusRoseburia

Lineage path7 lineage nodes

1Bacteria2Bacillati3Bacillota4Clostridia5Lachnospirales6Lachnospiraceae7Roseburia

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

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