Gene detail

NMF85_RS12780

Histidine kinase, Classic

Clostridioides difficile · GCF_024260145

Open genome Open selected cluster RefSeq

ClassHKTypeClassicLength530 aaTM0ValidatedNoCompleteYesContextpaired

Gene IDGCF_024260145#NMF85_RS12780Stable P2CS identifier used across views.

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

Selected clusterHKOC_1356136Run 6 · 16 sequences · id 100% · cov 80%

External referencesWP_045146670.1 · MIST4 NMF85_RS12780RefSeq · MIST4

Domain signature

Compact overview inferred from the domain field

HisKAHATPase_c

Protein length530 aaLength used to scale native and Biotite-like views.

Annotated domains22 with usable coordinates.

Domain coverage153 / 530 aa (28.9%)Merged over positioned domains only.

Domain description1 HisKA,1 HATPase_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 aa530 aa

Domain-by-domain annotation2 items

1 HisKA#1

309-375 aa · 67 aa · 12.6% of protein

Raw tokenHisKA:309:0.0000000000000129:375:67:64

2 HATPase_c#2

428-513 aa · 86 aa · 16.2% of protein

Raw tokenHATPase_c:428:0.000000092:513:90:109

Raw architecture: HisKA:309:0.0000000000000129:375:67:64#HATPase_c:428:0.000000092:513:90:109
Domain description: 1 HisKA,1 HATPase_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_JANCKV010000030.1::G00024

Group size22 locus tags listed below.

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

Context span4877-7154Genomic interval covered by the local TCS group.

Identifiers

Old locus tagNMF85_12720RefSeq proteinWP_045146670.1

Context group IDGCF_024260145::NZ_JANCKV010000030.1::G00024

Context members

NMF85_RS12775NMF85_RS12780

Partner locus tags

NMF85_RS12775NMF85_RS12780

Partner old locus tags

NMF85_12715NMF85_12720

Partner protein IDs

WP_004454617.1 WP_045146670.1

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_045146670.1.

Genomic coordinates

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

Current locus tagNMF85_RS12780Primary locus identifier stored in the genes table.

Old locus tagNMF85_12720Legacy locus tag recovered from the local context mapping.

Contig / repliconNZ_JANCKV010000030.1Sequence record reported by the local genomic context database.

Genomic interval5 562-7 154 nt1 593 nt · Forward (+)

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

Local TCS group span4 877-7 154 ntGCF_024260145::NZ_JANCKV010000030.1::G00024

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_JANCKV010000030.1::G00024

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_JANCKV010000030.1All displayed genes belong to this local TCS context.

Neighborhood span4 877-7 154 nt2 278 nt

Members21 current focus gene

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

4 877 nt7 154 nt

+-NMF85_RS12775 NMF85_RS12780

Neighborhood gene cards

2 genes in the current local neighborhood.

NMF85_RS12775GCF_024260145#NMF85_RS12775

RROmpR

4 877-5 593 nt · Forward (+)

Old locus NMF85_12715RefSeq WP_004454617.1

Open gene

NMF85_RS12780GCF_024260145#NMF85_RS12780

HKClassicCurrent focus

5 562-7 154 nt · Forward (+)

Old locus NMF85_12720RefSeq WP_045146670.1

Open current gene

Clusters

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

Available memberships1 cluster

HKOC_1356136HK

Run 616 sequencesid 100%cov 80%

PFAM HAMP + HisKA + HATPase_c

Representative GCF_001704795#DCQ01_RS00705

Selected clusterHKOC_1356136Run 6 · HK · 16 sequences

Representative sequenceGCF_001704795#DCQ01_RS00705Use this link to inspect the representative gene detail.

PFAM architectureHAMP + HisKA + HATPase_c3 domains in the representative PFAM annotation.

Open in cluster search Open representative gene

PFAM architecture for HKOC_1356136

Simplified PFAM architecture for HKOC_1356136

PFAM domain coverage: 190 / 530 aa (35.8%)

1 aa530 aa

HAMPHisKAHATPase_c

Simplified architecture: HAMP + HisKA + HATPase_c
Raw architecture: HAMP[255-295] | HisKA[310-375] | HATPase_c[427-509]
Domain count: 3
Matched identifier: HKOC_1356136
Positioned domains: HAMP 255-295 ; HisKA 310-375 ; HATPase_c 427-509

Cluster members and taxonomy

Representative gene: GCF_001704795#DCQ01_RS00705

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 HK genes NCBI assembly files

Related genes

Preview from the same derived genome key