Gene detail

HMPREF9475_RS05245

Response regulator, RpfG family

[Clostridium] symbiosum WAL-14673 · GCF_000189615

Open genome Open selected cluster RefSeq

ClassRRTypeRpfGLength696 aaTM0ValidatedNoCompleteYesContextorphan

Gene IDGCF_000189615#HMPREF9475_RS05245Stable P2CS identifier used across views.

GenomeGCF_000189615Bacteria; Bacillati; Bacillota; Clostridia; Lachnospirales; Lachnospiraceae; Lachnoclostridium

Selected clusterRROC_0030588Run 7 · 2 sequences · id 100% · cov 80% · representative

External referencesWP_003507096.1 · MIST4 HMPREF9475_RS05245RefSeq · MIST4

Domain signature

Compact overview inferred from the domain field

Response_regHDGGDEF

Protein length696 aaLength used to scale native and Biotite-like views.

Annotated domains33 with usable coordinates.

Domain coverage384 / 696 aa (55.2%)Merged over positioned domains only.

Domain description1 Response_reg,1 HD,1 GGDEFSummary 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 aa696 aa

Domain-by-domain annotation3 items

1 Response_reg#1

7-120 aa · 114 aa · 16.4% of protein

Raw tokenResponse_reg:7:4.32e-26:120:115:111

2 HD#2

181-299 aa · 119 aa · 17.1% of protein

Raw tokenHD:181:0.000000000000641:299:119:110

3 GGDEF#3

513-663 aa · 151 aa · 21.7% of protein

Raw tokenGGDEF:513:2.43e-42:663:160:160

Raw architecture: Response_reg:7:4.32e-26:120:115:111#HD:181:0.000000000000641:299:119:110#GGDEF:513:2.43e-42:663:160:160
Domain description: 1 Response_reg,1 HD,1 GGDEF
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_000189615::NZ_GL834358.1::G00020

Group size11 locus tag listed below.

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

Context span183589-185679Genomic interval covered by the local TCS group.

Identifiers

Old locus tagHMPREF9475_01029RefSeq proteinWP_003507096.1

Context group IDGCF_000189615::NZ_GL834358.1::G00020

Context members

HMPREF9475_RS05245

Partner locus tags

HMPREF9475_RS05245

Partner old locus tags

HMPREF9475_01029

Partner protein IDs

WP_003507096.1

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_003507096.1.

Genomic coordinates

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

Current locus tagHMPREF9475_RS05245Primary locus identifier stored in the genes table.

Old locus tagHMPREF9475_01029Legacy locus tag recovered from the local context mapping.

Contig / repliconNZ_GL834358.1Sequence record reported by the local genomic context database.

Genomic interval183 589-185 679 nt2 091 nt · Forward (+)

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

Local TCS group span183 589-185 679 ntGCF_000189615::NZ_GL834358.1::G00020

Quick actions

Open genome Search genes in genome

Local neighborhood

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

GCF_000189615::NZ_GL834358.1::G00020

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_GL834358.1All displayed genes belong to this local TCS context.

Neighborhood span183 589-185 679 nt2 091 nt

Members11 current focus gene

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

183 589 nt185 679 nt

+-HMPREF9475_RS05245

Neighborhood gene cards

1 gene in the current local neighborhood.

HMPREF9475_RS05245GCF_000189615#HMPREF9475_RS05245

RRRpfGCurrent focus

183 589-185 679 nt · Forward (+)

Old locus HMPREF9475_01029RefSeq WP_003507096.1

Open current gene

Clusters

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

Available memberships1 cluster

RROC_0030588RR

Run 72 sequencesid 100%cov 80%

PFAM Response_reg + HD_5 + GGDEF

Current gene is the representative sequence.

Selected clusterRROC_0030588Run 7 · RR · 2 sequences

Representative sequenceGCF_000189615#HMPREF9475_RS05245The current gene is the representative for this cluster.

PFAM architectureResponse_reg + HD_5 + GGDEF3 domains in the representative PFAM annotation.

Open in cluster search

PFAM architecture for RROC_0030588

Simplified PFAM architecture for RROC_0030588

PFAM domain coverage: 403 / 696 aa (57.9%)

1 aa696 aa

Response_regHD_5GGDEF

Simplified architecture: Response_reg + HD_5 + GGDEF
Raw architecture: Response_reg[7-119] | HD_5[179-318] | GGDEF[513-662]
Domain count: 3
Matched identifier: RROC_0030588
Positioned domains: Response_reg 7-119 ; Response_reg 7-119 ; HD_5 179-318 ; HD_5 179-318 ; GGDEF 513-662 ; GGDEF 513-662

Cluster members and taxonomy

Representative gene: GCF_000189615#HMPREF9475_RS05245

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

Genome taxonomy

Unknown

Taxonomy recordUnknownTaxon ID 742 741 · GCF_000189615

AssemblyClos_symb_WAL_14673_V2 · Scaffoldhaploid

Genome composition4 916 964 bp · 48,0% GC[Clostridium] symbiosum WAL-14673

Signal transduction countsGenes 109 · HK 55 · RR 50CheA 0 · PP 4

Ranked taxonomy7 ranked levels available

SuperkingdomBacteriaKingdomBacillatiPhylumBacillotaClassClostridiaOrderLachnospiralesFamilyLachnospiraceaeGenusLachnoclostridium

Lineage path7 lineage nodes

1Bacteria2Bacillati3Bacillota4Clostridia5Lachnospirales6Lachnospiraceae7Lachnoclostridium

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

Related genes

Preview from the same derived genome key