Gene detail

HMPREF1202_RS12575

Histidine kinase, Hybrid

[Ruminococcus] lactaris CC59_002D · GCF_000507785

Open genome Open selected cluster RefSeq UniProt

ClassHKTypeHybridLength922 aaTM0ValidatedNoCompleteYesContexttetrad

Gene IDGCF_000507785#HMPREF1202_RS12575Stable P2CS identifier used across views.

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

Selected clusterHKOC_0365341Run 6 · 4 sequences · id 100% · cov 80% · representative

External referencesWP_023923126.1 · A0A415D341 · MIST4 HMPREF1202_RS12575RefSeq · UniProt · MIST4

Domain signature

Compact overview inferred from the domain field

SBP_bac_3HisKAHATPase_cResponse_reg

Protein length922 aaLength used to scale native and Biotite-like views.

Annotated domains55 with usable coordinates.

Domain coverage722 / 922 aa (78.3%)Merged over positioned domains only.

Domain description2 SBP_bac_3,1 HisKA,1 HATPase_c,1 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 aa922 aa

Domain-by-domain annotation5 items

1 SBP_bac_3#1

39-257 aa · 219 aa · 23.8% of protein

Raw tokenSBP_bac_3:39:1.2e-29:257:230:224

2 SBP_bac_3#2

277-478 aa · 202 aa · 21.9% of protein

Raw tokenSBP_bac_3:277:0.0000000000000325:478:215:224

3 HisKA#3

545-610 aa · 66 aa · 7.2% of protein

Raw tokenHisKA:545:4.84e-18:610:66:64

4 HATPase_c#4

657-774 aa · 118 aa · 12.8% of protein

Raw tokenHATPase_c:657:6.29e-27:774:118:109

5 Response_reg#5

801-917 aa · 117 aa · 12.7% of protein

Raw tokenResponse_reg:801:2.25e-30:917:117:111

Raw architecture: SBP_bac_3:39:1.2e-29:257:230:224#SBP_bac_3:277:0.0000000000000325:478:215:224#HisKA:545:4.84e-18:610:66:64#HATPase_c:657:6.29e-27:774:118:109#Response_reg:801:2.25e-30:917:117:111
Domain description: 2 SBP_bac_3,1 HisKA,1 HATPase_c,1 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_02532RefSeq proteinWP_023923126.1

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_023923126.1Primary protein accession used for annex mappings.

UniProt accessionA0A415D341Primary UniProt accession resolved in the annex database.

UniProt IDA0A415D341_9FIRMDisplay identifier provided by UniProt.

GO / PubMed1 / 0Unique GO terms and literature references available below.

Reference hubs

Open RefSeq Open UniProt accession

GO terms

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_RS12575Primary locus identifier stored in the genes table.

Old locus tagHMPREF1202_02532Legacy locus tag recovered from the local context mapping.

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

Genomic interval35 237-38 005 nt2 769 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

HKHybridCurrent focus

35 237-38 005 nt · Reverse (-)

Old locus HMPREF1202_02532RefSeq WP_023923126.1

Open current gene

HMPREF1202_RS12580GCF_000507785#HMPREF1202_RS12580

HKHybrid

38 053-41 259 nt · Reverse (-)

Old locus HMPREF1202_02533RefSeq WP_044905675.1

Open gene

Clusters

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

Available memberships1 cluster

HKOC_0365341HK

Run 64 sequencesid 100%cov 80%

PFAM SBP_bac_3 + HisKA + HATPase_c + Response_reg

Current gene is the representative sequence.

Selected clusterHKOC_0365341Run 6 · HK · 4 sequences

Representative sequenceGCF_000507785#HMPREF1202_RS12575The current gene is the representative for this cluster.

PFAM architectureSBP_bac_3 + HisKA + HATPase_c + Response_reg4 domains in the representative PFAM annotation.

Open in cluster search

PFAM architecture for HKOC_0365341

Simplified PFAM architecture for HKOC_0365341

PFAM domain coverage: 504 / 922 aa (54.7%)

1 aa922 aa

SBP_bac_3HisKAHATPase_cResponse_reg

Simplified architecture: SBP_bac_3 + HisKA + HATPase_c + Response_reg
Raw architecture: SBP_bac_3[48-254] | HisKA[545-610] | HATPase_c[657-770] | Response_reg[801-917]
Domain count: 4
Matched identifier: HKOC_0365341
Positioned domains: SBP_bac_3 48-254 ; HisKA 545-610 ; HATPase_c 657-770 ; Response_reg 801-917

Cluster members and taxonomy

Representative gene: GCF_000507785#HMPREF1202_RS12575

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