Gene detail

DWY93_RS12270

Response regulator, RpfG family

Clostridium sp. AF28-12 · GCF_003435225

Open genome Open selected cluster RefSeq

ClassRRTypeRpfGLength685 aaTM0ValidatedNoCompleteYesContextorphan

Gene IDGCF_003435225#DWY93_RS12270Stable P2CS identifier used across views.

GenomeGCF_003435225Bacteria; Bacillati; Bacillota; Clostridia; Eubacteriales; Clostridiaceae; Clostridium

Selected clusterRROC_0032926Run 7 · 1 sequences · id 100% · cov 80% · representative

External referencesWP_117472391.1 · MIST4 DWY93_RS12270RefSeq · MIST4

Domain signature

Compact overview inferred from the domain field

GGDEFResponse_regHD

Protein length685 aaLength used to scale native and Biotite-like views.

Annotated domains33 with usable coordinates.

Domain coverage363 / 685 aa (53.0%)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 aa685 aa

Domain-by-domain annotation3 items

1 GGDEF#1

141-288 aa · 148 aa · 21.6% of protein

Raw tokenGGDEF:141:7.92e-38:288:159:160

2 Response_reg#2

315-427 aa · 113 aa · 16.5% of protein

Raw tokenResponse_reg:315:1.13e-24:427:114:111

3 HD#3

507-608 aa · 102 aa · 14.9% of protein

Raw tokenHD:507:0.0000000000000891:608:102:110

Raw architecture: GGDEF:141:7.92e-38:288:159:160#Response_reg:315:1.13e-24:427:114:111#HD:507:0.0000000000000891:608:102:110
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_003435225::NZ_QWGJ01000014.1::G00014

Group size11 locus tag listed below.

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

Context span79225-81282Genomic interval covered by the local TCS group.

Identifiers

Old locus tagDWY93_12275RefSeq proteinWP_117472391.1

Context group IDGCF_003435225::NZ_QWGJ01000014.1::G00014

Context members

DWY93_RS12270

Partner locus tags

DWY93_RS12270

Partner old locus tags

DWY93_12275

Partner protein IDs

WP_117472391.1

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_117472391.1.

Genomic coordinates

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

Current locus tagDWY93_RS12270Primary locus identifier stored in the genes table.

Old locus tagDWY93_12275Legacy locus tag recovered from the local context mapping.

Contig / repliconNZ_QWGJ01000014.1Sequence record reported by the local genomic context database.

Genomic interval79 225-81 282 nt2 058 nt · Reverse (-)

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

Local TCS group span79 225-81 282 ntGCF_003435225::NZ_QWGJ01000014.1::G00014

Quick actions

Open genome Search genes in genome

Local neighborhood

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

GCF_003435225::NZ_QWGJ01000014.1::G00014

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_QWGJ01000014.1All displayed genes belong to this local TCS context.

Neighborhood span79 225-81 282 nt2 058 nt

Members11 current focus gene

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

79 225 nt81 282 nt

+-DWY93_RS12270

Neighborhood gene cards

1 gene in the current local neighborhood.

DWY93_RS12270GCF_003435225#DWY93_RS12270

RRRpfGCurrent focus

79 225-81 282 nt · Reverse (-)

Old locus DWY93_12275RefSeq WP_117472391.1

Open current gene

Clusters

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

Available memberships1 cluster

RROC_0032926RR

Run 71 sequencesid 100%cov 80%

PFAM GGDEF + Response_reg + HD_5

Current gene is the representative sequence.

Selected clusterRROC_0032926Run 7 · RR · 1 sequences

Representative sequenceGCF_003435225#DWY93_RS12270The 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_0032926

Simplified PFAM architecture for RROC_0032926

PFAM domain coverage: 380 / 685 aa (55.5%)

1 aa685 aa

GGDEFResponse_regHD_5

Simplified architecture: GGDEF + Response_reg + HD_5
Raw architecture: GGDEF[142-287] | Response_reg[315-427] | HD_5[508-628]
Domain count: 3
Matched identifier: RROC_0032926
Positioned domains: GGDEF 142-287 ; GGDEF 142-287 ; Response_reg 315-427 ; Response_reg 315-427 ; HD_5 508-628 ; HD_5 508-628

Cluster members and taxonomy

Representative gene: GCF_003435225#DWY93_RS12270

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

Genome taxonomy

Unknown

Taxonomy recordUnknownTaxon ID 2 305 241 · GCF_003435225

AssemblyASM343522v1 · Scaffoldhaploid

Genome composition3 514 663 bp · 48,5% GCClostridium sp. AF28-12

Signal transduction countsGenes 67 · HK 31 · RR 34CheA 0 · PP 2

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