Gene detail

DW904_RS00395

Response regulator, unclassified

Ruminococcus sp. AM42-11 · GCF_003480145

Open genome Open selected cluster RefSeq

ClassRRTypeunclassifiedLength548 aaTM0ValidatedNoCompleteYesContextorphan

Gene IDGCF_003480145#DW904_RS00395Stable P2CS identifier used across views.

GenomeGCF_003480145Bacteria; Bacillati; Bacillota; Clostridia; Eubacteriales; Oscillospiraceae; Ruminococcus

Selected clusterRROC_0076688Run 7 · 4 sequences · id 100% · cov 80% · representative

External referencesWP_187565234.1 · MIST4 DW904_RS00395RefSeq · MIST4

Domain signature

Compact overview inferred from the domain field

Response_regHTH_AraC

Protein length548 aaLength used to scale native and Biotite-like views.

Annotated domains33 with usable coordinates.

Domain coverage192 / 548 aa (35.0%)Merged over positioned domains only.

Domain description1 Response_reg,2 HTH_AraCSummary 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 aa548 aa

Domain-by-domain annotation3 items

1 Response_reg#1

6-119 aa · 114 aa · 20.8% of protein

Raw tokenResponse_reg:6:2.46e-27:119:114:111

2 HTH_AraC#2

454-494 aa · 41 aa · 7.5% of protein

Raw tokenHTH_AraC:454:0.0000000195:494:41:42

3 HTH_AraC#3

509-545 aa · 37 aa · 6.8% of protein

Raw tokenHTH_AraC:509:0.00000879:545:37:42

Raw architecture: Response_reg:6:2.46e-27:119:114:111#HTH_AraC:454:0.0000000195:494:41:42#HTH_AraC:509:0.00000879:545:37:42
Domain description: 1 Response_reg,2 HTH_AraC
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_003480145::NZ_QUIO01000001.1::G00004

Group size11 locus tag listed below.

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

Context span92224-93870Genomic interval covered by the local TCS group.

Identifiers

Old locus tagDW904_00395RefSeq proteinWP_187565234.1

Context group IDGCF_003480145::NZ_QUIO01000001.1::G00004

Context members

DW904_RS00395

Partner locus tags

DW904_RS00395

Partner old locus tags

DW904_00395

Partner protein IDs

WP_187565234.1

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_187565234.1.

Genomic coordinates

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

Current locus tagDW904_RS00395Primary locus identifier stored in the genes table.

Old locus tagDW904_00395Legacy locus tag recovered from the local context mapping.

Contig / repliconNZ_QUIO01000001.1Sequence record reported by the local genomic context database.

Genomic interval92 224-93 870 nt1 647 nt · Reverse (-)

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

Local TCS group span92 224-93 870 ntGCF_003480145::NZ_QUIO01000001.1::G00004

Quick actions

Open genome Search genes in genome

Local neighborhood

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

GCF_003480145::NZ_QUIO01000001.1::G00004

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_QUIO01000001.1All displayed genes belong to this local TCS context.

Neighborhood span92 224-93 870 nt1 647 nt

Members11 current focus gene

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

92 224 nt93 870 nt

+-DW904_RS00395

Neighborhood gene cards

1 gene in the current local neighborhood.

DW904_RS00395GCF_003480145#DW904_RS00395

RRunclassifiedCurrent focus

92 224-93 870 nt · Reverse (-)

Old locus DW904_00395RefSeq WP_187565234.1

Open current gene

Clusters

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

Available memberships1 cluster

RROC_0076688RR

Run 74 sequencesid 100%cov 80%

PFAM Response_reg + GGDEF_2 + HTH_18

Current gene is the representative sequence.

Selected clusterRROC_0076688Run 7 · RR · 4 sequences

Representative sequenceGCF_003480145#DW904_RS00395The current gene is the representative for this cluster.

PFAM architectureResponse_reg + GGDEF_2 + HTH_183 domains in the representative PFAM annotation.

Open in cluster search

PFAM architecture for RROC_0076688

Simplified PFAM architecture for RROC_0076688

PFAM domain coverage: 280 / 548 aa (51.1%)

1 aa548 aa

Response_regGGDEF_2HTH_18

Simplified architecture: Response_reg + GGDEF_2 + HTH_18
Raw architecture: Response_reg[6-118] | GGDEF_2[224-312] | HTH_18[468-545]
Domain count: 3
Matched identifier: RROC_0076688
Positioned domains: Response_reg 6-118 ; Response_reg 6-118 ; GGDEF_2 224-312 ; GGDEF_2 224-312 ; HTH_18 468-545 ; HTH_18 468-545

Cluster members and taxonomy

Representative gene: GCF_003480145#DW904_RS00395

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

Genome taxonomy

Unknown

Taxonomy recordUnknownTaxon ID 2 292 372 · GCF_003480145

AssemblyASM348014v1 · Contighaploid

Genome composition4 698 861 bp · 42,5% GCRuminococcus sp. AM42-11

Signal transduction countsGenes 130 · HK 64 · RR 63CheA 0 · PP 3

Ranked taxonomy7 ranked levels available

SuperkingdomBacteriaKingdomBacillatiPhylumBacillotaClassClostridiaOrderEubacterialesFamilyOscillospiraceaeGenusRuminococcus

Lineage path7 lineage nodes

1Bacteria2Bacillati3Bacillota4Clostridia5Eubacteriales6Oscillospiraceae7Ruminococcus

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

Related genes

Preview from the same derived genome key