Gene detail

HMPREF1202_RS12580

Histidine kinase, Hybrid

[Ruminococcus] lactaris CC59_002D · GCF_000507785

Open genome Open selected cluster RefSeq UniProt

ClassHKTypeHybridLength1068 aaTM0ValidatedNoCompleteYesContexttetrad

Gene IDGCF_000507785#HMPREF1202_RS12580Stable P2CS identifier used across views.

GenomeGCF_000507785Bacteria; Bacillati; Bacillota; Clostridia; Lachnospirales; Lachnospiraceae; Mediterraneibacter

Selected clusterHKOC_0247569Run 6 · 4 sequences · id 100% · cov 80% · representative

External referencesWP_044905675.1 · A0A415D373 · MIST4 HMPREF1202_RS12580RefSeq · UniProt · MIST4

Domain signature

Compact overview inferred from the domain field

PAS_3HisKAHATPase_cResponse_reg

Protein length1068 aaLength used to scale native and Biotite-like views.

Annotated domains55 with usable coordinates.

Domain coverage505 / 1068 aa (47.3%)Merged over positioned domains only.

Domain description1 PAS_3,1 HisKA,1 HATPase_c,2 Response_regSummary 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 aa1068 aa

Domain-by-domain annotation5 items

1 PAS_3#1

168-256 aa · 89 aa · 8.3% of protein

Raw tokenPAS_3:168:7.56e-19:256:89:89

2 HisKA#2

558-624 aa · 67 aa · 6.3% of protein

Raw tokenHisKA:558:1.9e-16:624:67:64

3 HATPase_c#3

671-785 aa · 115 aa · 10.8% of protein

Raw tokenHATPase_c:671:9.44e-31:785:115:109

4 Response_reg#4

805-921 aa · 117 aa · 11.0% of protein

Raw tokenResponse_reg:805:6.24e-20:921:117:111

5 Response_reg#5

949-1065 aa · 117 aa · 11.0% of protein

Raw tokenResponse_reg:949:6.44e-30:1065:117:111

Raw architecture: PAS_3:168:7.56e-19:256:89:89#HisKA:558:1.9e-16:624:67:64#HATPase_c:671:9.44e-31:785:115:109#Response_reg:805:6.24e-20:921:117:111#Response_reg:949:6.44e-30:1065:117:111
Domain description: 1 PAS_3,1 HisKA,1 HATPase_c,2 Response_reg
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 labeltetradGCF_000507785::NZ_KI669411.1::G00026

Group size44 locus tags listed below.

HK / RR3 / 1Counts resolved for the local TCS neighborhood.

Context span33996-41259Genomic interval covered by the local TCS group.

Identifiers

Old locus tagHMPREF1202_02533RefSeq proteinWP_044905675.1

Context group IDGCF_000507785::NZ_KI669411.1::G00026

Context members

HMPREF1202_RS16560HMPREF1202_RS12570HMPREF1202_RS12575HMPREF1202_RS12580

Partner locus tags

HMPREF1202_RS16560HMPREF1202_RS12570HMPREF1202_RS12575HMPREF1202_RS12580

Partner old locus tags

HMPREF1202_02530HMPREF1202_02531HMPREF1202_02532HMPREF1202_02533

Partner protein IDs

WP_023923124.1 WP_023923125.1 WP_023923126.1 WP_044905675.1

External references

Resolved via p2cs_annexes.db when the RefSeq protein is present in the annex table

RefSeqWP_044905675.1Primary protein accession used for annex mappings.

UniProt accessionA0A415D373Primary UniProt accession resolved in the annex database.

UniProt IDA0A415D373_9FIRMDisplay identifier provided by UniProt.

GO / PubMed2 / 0Unique GO terms and literature references available below.

Reference hubs

Open RefSeq Open UniProt accession

GO terms

GO:0016020 GO:0000155

Genomic coordinates

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

Current locus tagHMPREF1202_RS12580Primary locus identifier stored in the genes table.

Old locus tagHMPREF1202_02533Legacy locus tag recovered from the local context mapping.

Contig / repliconNZ_KI669411.1Sequence record reported by the local genomic context database.

Genomic interval38 053-41 259 nt3 207 nt · Reverse (-)

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

Local TCS group span33 996-41 259 ntGCF_000507785::NZ_KI669411.1::G00026

Quick actions

Open genome Search genes in genome

Local neighborhood

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

GCF_000507785::NZ_KI669411.1::G00026

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 labeltetradNeighborhood members are ordered by genomic coordinates.

Contig / repliconNZ_KI669411.1All displayed genes belong to this local TCS context.

Neighborhood span33 996-41 259 nt7 264 nt

Members41 current focus gene

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

33 996 nt41 259 nt

+-HMPREF1202_RS12570 HMPREF1202_RS12575 HMPREF1202_RS12580

Neighborhood gene cards

4 genes in the current local neighborhood.

HMPREF1202_RS16560GCF_000507785#HMPREF1202_RS16560

RRCheY

33 996-34 229 nt · Reverse (-)

Old locus HMPREF1202_02530RefSeq WP_023923124.1

Open gene

HMPREF1202_RS12570GCF_000507785#HMPREF1202_RS12570

HKClassic

34 284-35 102 nt · Reverse (-)

Old locus HMPREF1202_02531RefSeq WP_023923125.1

Open gene

HMPREF1202_RS12575GCF_000507785#HMPREF1202_RS12575

HKHybrid

35 237-38 005 nt · Reverse (-)

Old locus HMPREF1202_02532RefSeq WP_023923126.1

Open gene

HMPREF1202_RS12580GCF_000507785#HMPREF1202_RS12580

HKHybridCurrent focus

38 053-41 259 nt · Reverse (-)

Old locus HMPREF1202_02533RefSeq WP_044905675.1

Open current gene

Clusters

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

Available memberships1 cluster

HKOC_0247569HK

Run 64 sequencesid 100%cov 80%

PFAM PAS_3 + HisKA + HATPase_c + Response_reg + Response_reg

Current gene is the representative sequence.

Selected clusterHKOC_0247569Run 6 · HK · 4 sequences

Representative sequenceGCF_000507785#HMPREF1202_RS12580The current gene is the representative for this cluster.

PFAM architecturePAS_3 + HisKA + HATPase_c + Response_reg + Response_reg5 domains in the representative PFAM annotation.

Open in cluster search

PFAM architecture for HKOC_0247569

Simplified PFAM architecture for HKOC_0247569

PFAM domain coverage: 506 / 1068 aa (47.4%)

1 aa1068 aa

PAS_3HisKAHATPase_cResponse_regResponse_reg

Simplified architecture: PAS_3 + HisKA + HATPase_c + Response_reg + Response_reg
Raw architecture: PAS_3[167-256] | HisKA[558-624] | HATPase_c[671-787] | Response_reg[805-920] | Response_reg[949-1064]
Domain count: 5
Matched identifier: HKOC_0247569
Positioned domains: PAS_3 167-256 ; HisKA 558-624 ; HATPase_c 671-787 ; Response_reg 805-920 ; Response_reg 949-1064

Cluster members and taxonomy

Representative gene: GCF_000507785#HMPREF1202_RS12580

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

Genome taxonomy

Unknown

Taxonomy recordUnknownTaxon ID 1 073 376 · GCF_000507785

AssemblyRumi_lact_CC59_002D_V1 · Scaffoldhaploid

Genome composition3 086 899 bp · 42,5% GC[Ruminococcus] lactaris CC59_002D

Signal transduction countsGenes 54 · HK 27 · RR 27CheA 0 · PP 0

Ranked taxonomy7 ranked levels available

SuperkingdomBacteriaKingdomBacillatiPhylumBacillotaClassClostridiaOrderLachnospiralesFamilyLachnospiraceaeGenusMediterraneibacter

Lineage path7 lineage nodes

1Bacteria2Bacillati3Bacillota4Clostridia5Lachnospirales6Lachnospiraceae7Mediterraneibacter

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

Related genes

Preview from the same derived genome key