Gene detail

PMZ67_RS01640

Histidine kinase, Hybrid

[Clostridium] symbiosum · GCF_028207305

Open genome Open selected cluster RefSeq UniProt

ClassHKTypeHybridLength1312 aaTM0ValidatedNoCompleteYesContextorphan

Gene IDGCF_028207305#PMZ67_RS01640Stable P2CS identifier used across views.

GenomeGCF_028207305Bacteria; Bacillati; Bacillota; Clostridia; Lachnospirales; Lachnospiraceae; Lachnoclostridium

Selected clusterHKOC_0120000Run 6 · 7 sequences · id 100% · cov 80% · representative

External referencesWP_272120354.1 · A0AAW6AME7 · MIST4 PMZ67_RS01640RefSeq · UniProt · MIST4

Domain signature

Compact overview inferred from the domain field

PAS_3HisKAHATPase_cResponse_reg

Protein length1312 aaLength used to scale native and Biotite-like views.

Annotated domains77 with usable coordinates.

Domain coverage616 / 1312 aa (47.0%)Merged over positioned domains only.

Domain description4 PAS_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 aa1312 aa

Domain-by-domain annotation7 items

1 PAS_3#1

165-243 aa · 79 aa · 6.0% of protein

Raw tokenPAS_3:165:0.0000000000681:243:84:89

2 PAS_3#2

302-390 aa · 89 aa · 6.8% of protein

Raw tokenPAS_3:302:0.0000000000000144:390:90:89

3 PAS_3#3

448-519 aa · 72 aa · 5.5% of protein

Raw tokenPAS_3:448:0.00000437:519:74:89

4 PAS_3#4

559-631 aa · 73 aa · 5.6% of protein

Raw tokenPAS_3:559:0.000000172:631:74:89

5 HisKA#5

936-1002 aa · 67 aa · 5.1% of protein

Raw tokenHisKA:936:2.24e-19:1002:67:64

6 HATPase_c#6

1048-1165 aa · 118 aa · 9.0% of protein

Raw tokenHATPase_c:1048:5.38e-29:1165:119:109

7 Response_reg#7

1190-1307 aa · 118 aa · 9.0% of protein

Raw tokenResponse_reg:1190:2.96e-30:1307:118:111

Raw architecture: PAS_3:165:0.0000000000681:243:84:89#PAS_3:302:0.0000000000000144:390:90:89#PAS_3:448:0.00000437:519:74:89#PAS_3:559:0.000000172:631:74:89#HisKA:936:2.24e-19:1002:67:64#HATPase_c:1048:5.38e-29:1165:119:109#Response_reg:1190:2.96e-30:1307:118:111
Domain description: 4 PAS_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 labelorphanGCF_028207305::NZ_JAQLGN010000002.1::G00024

Group size11 locus tag listed below.

HK / RR1 / 0Counts resolved for the local TCS neighborhood.

Context span129147-133085Genomic interval covered by the local TCS group.

Identifiers

Old locus tagPMZ67_01640RefSeq proteinWP_272120354.1

Context group IDGCF_028207305::NZ_JAQLGN010000002.1::G00024

Context members

PMZ67_RS01640

Partner locus tags

PMZ67_RS01640

Partner old locus tags

PMZ67_01640

Partner protein IDs

WP_272120354.1

External references

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

RefSeqWP_272120354.1Primary protein accession used for annex mappings.

UniProt accessionA0AAW6AME7Primary UniProt accession resolved in the annex database.

UniProt IDA0AAW6AME7_CLOSYDisplay identifier provided by UniProt.

GO / PubMed3 / 0Unique GO terms and literature references available below.

Reference hubs

Open RefSeq Open UniProt accession

GO terms

GO:0005886 GO:0009927 GO:0000155

Genomic coordinates

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

Current locus tagPMZ67_RS01640Primary locus identifier stored in the genes table.

Old locus tagPMZ67_01640Legacy locus tag recovered from the local context mapping.

Contig / repliconNZ_JAQLGN010000002.1Sequence record reported by the local genomic context database.

Genomic interval129 147-133 085 nt3 939 nt · Forward (+)

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

Local TCS group span129 147-133 085 ntGCF_028207305::NZ_JAQLGN010000002.1::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_028207305::NZ_JAQLGN010000002.1::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 labelorphanNeighborhood members are ordered by genomic coordinates.

Contig / repliconNZ_JAQLGN010000002.1All displayed genes belong to this local TCS context.

Neighborhood span129 147-133 085 nt3 939 nt

Members11 current focus gene

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

129 147 nt133 085 nt

+-PMZ67_RS01640

Neighborhood gene cards

1 gene in the current local neighborhood.

PMZ67_RS01640GCF_028207305#PMZ67_RS01640

HKHybridCurrent focus

129 147-133 085 nt · Forward (+)

Old locus PMZ67_01640RefSeq WP_272120354.1

Open current gene

Clusters

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

Available memberships1 cluster

HKOC_0120000HK

Run 67 sequencesid 100%cov 80%

PFAM PAS_3 + PAS_3 + HisKA + HATPase_c + Response_reg

Current gene is the representative sequence.

Selected clusterHKOC_0120000Run 6 · HK · 7 sequences

Representative sequenceGCF_028207305#PMZ67_RS01640The current gene is the representative for this cluster.

PFAM architecturePAS_3 + PAS_3 + HisKA + HATPase_c + Response_reg5 domains in the representative PFAM annotation.

Open in cluster search

PFAM architecture for HKOC_0120000

Simplified PFAM architecture for HKOC_0120000

PFAM domain coverage: 469 / 1312 aa (35.7%)

1 aa1312 aa

PAS_3PAS_3HisKAHATPase_cResponse_reg

Simplified architecture: PAS_3 + PAS_3 + HisKA + HATPase_c + Response_reg
Raw architecture: PAS_3[165-245] | PAS_3[303-389] | HisKA[936-1002] | HATPase_c[1048-1165] | Response_reg[1190-1305]
Domain count: 5
Matched identifier: HKOC_0120000
Positioned domains: PAS_3 165-245 ; PAS_3 303-389 ; HisKA 936-1002 ; HATPase_c 1048-1165 ; Response_reg 1190-1305

Cluster members and taxonomy

Representative gene: GCF_028207305#PMZ67_RS01640

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

Genome taxonomy

Unknown

Taxonomy recordUnknownTaxon ID 1 512 · GCF_028207305

AssemblyASM2820730v1 · Scaffoldhaploid

Genome composition5 103 156 bp · 47,5% GC[Clostridium] symbiosum

Signal transduction countsGenes 118 · HK 59 · RR 56CheA 1 · PP 3

Ranked taxonomy7 ranked levels available

SuperkingdomBacteriaKingdomBacillatiPhylumBacillotaClassClostridiaOrderLachnospiralesFamilyLachnospiraceaeGenusLachnoclostridium

Lineage path7 lineage nodes

1Bacteria2Bacillati3Bacillota4Clostridia5Lachnospirales6Lachnospiraceae7Lachnoclostridium

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

Related genes

Preview from the same derived genome key