Gene detail

NMF85_RS13390

Response regulator OmpR family

Clostridioides difficile · GCF_024260145

Open genome Open selected cluster RefSeq

ClassRRTypeOmpRLength234 aaTM0ValidatedNoCompleteYesContextpaired

Gene IDGCF_024260145#NMF85_RS13390Stable P2CS identifier used across views.

GenomeGCF_024260145Bacteria; Bacillati; Bacillota; Clostridia; Peptostreptococcales; Peptostreptococcaceae; Clostridioides

Selected clusterRROC_1049065Run 7 · 41 sequences · id 100% · cov 80%

External referencesWP_021374494.1 · MIST4 NMF85_RS13390RefSeq · MIST4

Domain signature

Compact overview inferred from the domain field

Response_regTrans_reg_C

Protein length234 aaLength used to scale native and Biotite-like views.

Annotated domains22 with usable coordinates.

Domain coverage188 / 234 aa (80.3%)Merged over positioned domains only.

Domain description1 Response_reg,1 Trans_reg_CSummary 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 aa234 aa

Domain-by-domain annotation2 items

1 Response_reg#1

7-117 aa · 111 aa · 47.4% of protein

Raw tokenResponse_reg:7:2.27e-34:117:111:111

2 Trans_reg_C#2

155-231 aa · 77 aa · 32.9% of protein

Raw tokenTrans_reg_C:155:2.36e-26:231:77:77

Raw architecture: Response_reg:7:2.27e-34:117:111:111#Trans_reg_C:155:2.36e-26:231:77:77
Domain description: 1 Response_reg,1 Trans_reg_C
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 labelpairedGCF_024260145::NZ_JANCKV010000032.1::G00028

Group size22 locus tags listed below.

HK / RR1 / 1Counts resolved for the local TCS neighborhood.

Context span35833-38135Genomic interval covered by the local TCS group.

Identifiers

Old locus tagNMF85_13330RefSeq proteinWP_021374494.1

Context group IDGCF_024260145::NZ_JANCKV010000032.1::G00028

Context members

NMF85_RS13385NMF85_RS13390

Partner locus tags

NMF85_RS13385NMF85_RS13390

Partner old locus tags

NMF85_13325NMF85_13330

Partner protein IDs

WP_021374542.1 WP_021374494.1

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_021374494.1.

Genomic coordinates

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

Current locus tagNMF85_RS13390Primary locus identifier stored in the genes table.

Old locus tagNMF85_13330Legacy locus tag recovered from the local context mapping.

Contig / repliconNZ_JANCKV010000032.1Sequence record reported by the local genomic context database.

Genomic interval37 431-38 135 nt705 nt · Forward (+)

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

Local TCS group span35 833-38 135 ntGCF_024260145::NZ_JANCKV010000032.1::G00028

Quick actions

Open genome Search genes in genome

Local neighborhood

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

GCF_024260145::NZ_JANCKV010000032.1::G00028

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 labelpairedNeighborhood members are ordered by genomic coordinates.

Contig / repliconNZ_JANCKV010000032.1All displayed genes belong to this local TCS context.

Neighborhood span35 833-38 135 nt2 303 nt

Members21 current focus gene

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

35 833 nt38 135 nt

+-NMF85_RS13385 NMF85_RS13390

Neighborhood gene cards

2 genes in the current local neighborhood.

NMF85_RS13385GCF_024260145#NMF85_RS13385

HKClassic

35 833-37 440 nt · Forward (+)

Old locus NMF85_13325RefSeq WP_021374542.1

Open gene

NMF85_RS13390GCF_024260145#NMF85_RS13390

RROmpRCurrent focus

37 431-38 135 nt · Forward (+)

Old locus NMF85_13330RefSeq WP_021374494.1

Open current gene

Clusters

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

Available memberships1 cluster

RROC_1049065RR

Run 741 sequencesid 100%cov 80%

PFAM Response_reg + Trans_reg_C

Representative GCF_000449185#QCW_RS02615

Selected clusterRROC_1049065Run 7 · RR · 41 sequences

Representative sequenceGCF_000449185#QCW_RS02615Use this link to inspect the representative gene detail.

PFAM architectureResponse_reg + Trans_reg_C2 domains in the representative PFAM annotation.

Open in cluster search Open representative gene

PFAM architecture for RROC_1049065

Simplified PFAM architecture for RROC_1049065

PFAM domain coverage: 187 / 234 aa (79.9%)

1 aa234 aa

Response_regTrans_reg_C

Simplified architecture: Response_reg + Trans_reg_C
Raw architecture: Response_reg[7-117] | Trans_reg_C[156-231]
Domain count: 2
Matched identifier: RROC_1049065
Positioned domains: Response_reg 7-117 ; Response_reg 7-117 ; Trans_reg_C 156-231 ; Trans_reg_C 156-231

Cluster members and taxonomy

Representative gene: GCF_000449185#QCW_RS02615

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

Genome taxonomy

Unknown

Taxonomy recordUnknownTaxon ID 1 496 · GCF_024260145

AssemblyASM2426014v1 · Contighaploid

Genome composition4 130 739 bp · 28,5% GCClostridioides difficile

Signal transduction countsGenes 90 · HK 41 · RR 47CheA 1 · PP 2

Ranked taxonomy7 ranked levels available

SuperkingdomBacteriaKingdomBacillatiPhylumBacillotaClassClostridiaOrderPeptostreptococcalesFamilyPeptostreptococcaceaeGenusClostridioides

Lineage path7 lineage nodes

1Bacteria2Bacillati3Bacillota4Clostridia5Peptostreptococcales6Peptostreptococcaceae7Clostridioides

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

Related genes

Preview from the same derived genome key