Gene detail

DW904_RS01335

Response regulator, unclassified

Ruminococcus sp. AM42-11 · GCF_003480145

Open genome Open selected cluster RefSeq

ClassRRTypeunclassifiedLength540 aaTM0ValidatedNoCompleteYesContextorphan

Gene IDGCF_003480145#DW904_RS01335Stable P2CS identifier used across views.

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

Selected clusterRROC_0089816Run 7 · 1 sequences · id 100% · cov 80% · representative

External referencesWP_118577755.1 · MIST4 DW904_RS01335RefSeq · MIST4

Domain signature

Compact overview inferred from the domain field

Response_regHTH_AraC

Protein length540 aaLength used to scale native and Biotite-like views.

Annotated domains22 with usable coordinates.

Domain coverage155 / 540 aa (28.7%)Merged over positioned domains only.

Domain description1 Response_reg,1 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 aa540 aa

Domain-by-domain annotation2 items

1 Response_reg#1

4-116 aa · 113 aa · 20.9% of protein

Raw tokenResponse_reg:4:1.81e-24:116:113:111

2 HTH_AraC#2

443-484 aa · 42 aa · 7.8% of protein

Raw tokenHTH_AraC:443:0.00000756:484:42:42

Raw architecture: Response_reg:4:1.81e-24:116:113:111#HTH_AraC:443:0.00000756:484:42:42
Domain description: 1 Response_reg,1 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::G00013

Group size11 locus tag listed below.

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

Context span316270-317892Genomic interval covered by the local TCS group.

Identifiers

Old locus tagDW904_01335RefSeq proteinWP_118577755.1

Context group IDGCF_003480145::NZ_QUIO01000001.1::G00013

Context members

DW904_RS01335

Partner locus tags

DW904_RS01335

Partner old locus tags

DW904_01335

Partner protein IDs

WP_118577755.1

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_118577755.1.

Genomic coordinates

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

Current locus tagDW904_RS01335Primary locus identifier stored in the genes table.

Old locus tagDW904_01335Legacy locus tag recovered from the local context mapping.

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

Genomic interval316 270-317 892 nt1 623 nt · Reverse (-)

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

Local TCS group span316 270-317 892 ntGCF_003480145::NZ_QUIO01000001.1::G00013

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::G00013

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 span316 270-317 892 nt1 623 nt

Members11 current focus gene

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

316 270 nt317 892 nt

+-DW904_RS01335

Neighborhood gene cards

1 gene in the current local neighborhood.

DW904_RS01335GCF_003480145#DW904_RS01335

RRunclassifiedCurrent focus

316 270-317 892 nt · Reverse (-)

Old locus DW904_01335RefSeq WP_118577755.1

Open current gene

Clusters

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

Available memberships1 cluster

RROC_0089816RR

Run 71 sequencesid 100%cov 80%

PFAM Response_reg + GGDEF_2 + HTH_18

Current gene is the representative sequence.

Selected clusterRROC_0089816Run 7 · RR · 1 sequences

Representative sequenceGCF_003480145#DW904_RS01335The 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_0089816

Simplified PFAM architecture for RROC_0089816

PFAM domain coverage: 323 / 540 aa (59.8%)

1 aa540 aa

Response_regGGDEF_2HTH_18

Simplified architecture: Response_reg + GGDEF_2 + HTH_18
Raw architecture: Response_reg[4-116] | GGDEF_2[169-300] | HTH_18[458-535]
Domain count: 3
Matched identifier: RROC_0089816
Positioned domains: Response_reg 4-116 ; Response_reg 4-116 ; GGDEF_2 169-300 ; GGDEF_2 169-300 ; HTH_18 458-535 ; HTH_18 458-535

Cluster members and taxonomy

Representative gene: GCF_003480145#DW904_RS01335

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

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