Gene detail

NMF85_RS07455

Response regulator OmpR family

Clostridioides difficile · GCF_024260145

Open genome Open selected cluster RefSeq

ClassRRTypeOmpRLength230 aaTM0ValidatedNoCompleteYesContextpaired

Gene IDGCF_024260145#NMF85_RS07455Stable P2CS identifier used across views.

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

Selected clusterRROC_1202423Run 7 · 39 sequences · id 100% · cov 80%

External referencesWP_021376721.1 · MIST4 NMF85_RS07455RefSeq · MIST4

Domain signature

Compact overview inferred from the domain field

Response_regTrans_reg_C

Protein length230 aaLength used to scale native and Biotite-like views.

Annotated domains22 with usable coordinates.

Domain coverage187 / 230 aa (81.3%)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 aa230 aa

Domain-by-domain annotation2 items

1 Response_reg#1

5-114 aa · 110 aa · 47.8% of protein

Raw tokenResponse_reg:5:5.85e-38:114:111:111

2 Trans_reg_C#2

152-228 aa · 77 aa · 33.5% of protein

Raw tokenTrans_reg_C:152:8.13e-32:228:77:77

Raw architecture: Response_reg:5:5.85e-38:114:111:111#Trans_reg_C:152:8.13e-32:228:77:77
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_JANCKV010000014.1::G00006

Group size22 locus tags listed below.

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

Context span30646-32509Genomic interval covered by the local TCS group.

Identifiers

Old locus tagNMF85_07445RefSeq proteinWP_021376721.1

Context group IDGCF_024260145::NZ_JANCKV010000014.1::G00006

Context members

NMF85_RS07455NMF85_RS07460

Partner locus tags

NMF85_RS07455NMF85_RS07460

Partner old locus tags

NMF85_07445NMF85_07450

Partner protein IDs

WP_021376721.1 WP_032547807.1

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_021376721.1.

Genomic coordinates

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

Current locus tagNMF85_RS07455Primary locus identifier stored in the genes table.

Old locus tagNMF85_07445Legacy locus tag recovered from the local context mapping.

Contig / repliconNZ_JANCKV010000014.1Sequence record reported by the local genomic context database.

Genomic interval30 646-31 338 nt693 nt · Forward (+)

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

Local TCS group span30 646-32 509 ntGCF_024260145::NZ_JANCKV010000014.1::G00006

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_JANCKV010000014.1::G00006

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_JANCKV010000014.1All displayed genes belong to this local TCS context.

Neighborhood span30 646-32 509 nt1 864 nt

Members21 current focus gene

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

30 646 nt32 509 nt

+-NMF85_RS07455 NMF85_RS07460

Neighborhood gene cards

2 genes in the current local neighborhood.

NMF85_RS07455GCF_024260145#NMF85_RS07455

RROmpRCurrent focus

30 646-31 338 nt · Forward (+)

Old locus NMF85_07445RefSeq WP_021376721.1

Open current gene

NMF85_RS07460GCF_024260145#NMF85_RS07460

HKClassic

31 328-32 509 nt · Forward (+)

Old locus NMF85_07450RefSeq WP_032547807.1

Open gene

Clusters

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

Available memberships1 cluster

RROC_1202423RR

Run 739 sequencesid 100%cov 80%

PFAM Response_reg + Trans_reg_C

Representative GCF_000449185#QCW_RS18045

Selected clusterRROC_1202423Run 7 · RR · 39 sequences

Representative sequenceGCF_000449185#QCW_RS18045Use 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_1202423

Simplified PFAM architecture for RROC_1202423

PFAM domain coverage: 185 / 230 aa (80.4%)

1 aa230 aa

Response_regTrans_reg_C

Simplified architecture: Response_reg + Trans_reg_C
Raw architecture: Response_reg[5-113] | Trans_reg_C[152-227]
Domain count: 2
Matched identifier: RROC_1202423
Positioned domains: Response_reg 5-113 ; Response_reg 5-113 ; Trans_reg_C 152-227 ; Trans_reg_C 152-227

Cluster members and taxonomy

Representative gene: GCF_000449185#QCW_RS18045

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