Gene detail

ABID56_RS04515

Probable incomplete histidine kinase

Alkalibacillus flavidus · GCF_040545925

Open genome Open selected cluster

ClassHKTypeClassicLength529 aaTM2ValidatedNoCompleteNoContextNo local context

Gene IDGCF_040545925#ABID56_RS04515Stable P2CS identifier used across views.

GenomeGCF_040545925Unknown

Selected clusterIHKOC_451327Run 0 · 2 sequences · id 100% · cov 80%

External referencesMIST4 ABID56_RS04515MIST4

Domain signature

Compact overview inferred from the domain field

PAS_9HATPase_cHisKA_LIKE92 TM helicesNew HisKA: HisKA_LIKE9

Protein length529 aaLength used to scale native and Biotite-like views.

New HisKA domainHisKA_LIKE9331-397 aa · independent E-value 1.10e-21

Annotated domains33 with usable coordinates.

Domain coverage262 / 529 aa (49.5%)Merged over positioned domains only.

Domain description1 PAS_9,1 HATPase_cSummary string stored in the genes table.

Signal peptideNot predictedFrom HK/TM SQLite database.

Transmembrane helices11-34 aa · 24 aa · 172-194 aa · 23 aa2 helices reported by HK/TM SQLite database.

Complete domain annotations

Domain view

Native Biotite-like

Native P2CS viewFrontend rendering from the parsed domain string and TMPRED protein features.

1 aa529 aa

Domain-by-domain annotation3 items

1 PAS_9#1

224-313 aa · 90 aa · 17.0% of protein

Raw tokenPAS_9:224:0.00000224:313:101:102

2 HATPase_c#2

422-526 aa · 105 aa · 19.8% of protein

Raw tokenHATPase_c:422:1.64e-21:526:106:109

3 HisKA_LIKE9 (new HisKA)#3

331-397 aa · 67 aa · 12.7% of protein

Raw tokenHisKA_LIKE9[331-397]

Raw architecture: PAS_9:224:0.00000224:313:101:102#HATPase_c:422:1.64e-21:526:106:109
Domain description: 1 PAS_9,1 HATPase_c
New HisKA annotation: HisKA_LIKE9 (331-397 aa)
TM description: N/A
TMPRED source: HK/TM SQLite database
TMPRED segments: TM helix 11-34; TM helix 172-194
Complete: No

Protein sequence

On-demand local amino-acid sequence in FASTA format

Context mapping

Resolved via p2cs_tcs_context.db when a locus tag match exists

No local TCS context mapping is available for this gene.

External references

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

No external UniProt / GO / PubMed mapping is available for this gene.

Genomic coordinates

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

Current locus tagABID56_RS04515Primary locus identifier stored in the genes table.

Old locus tagUnavailableNo previous locus tag available for this gene.

Contig / repliconUnavailableNo contig or replicon mapping is available for this gene.

Genomic intervalUnavailableNo start/end genomic coordinates are available for this gene.

StrandUnavailableStrand sign follows the local context database convention.

Local TCS group spanUnavailableNo grouped neighborhood span is available for this gene.

Quick actions

Open genome Search genes in genome

Genome neighborhood

Gene-centered window parsed directly from the configured gzipped GFF annotation

GCF_040545925 · NZ_JBEPMX010000003.1

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.

Centered locusABID56_RS0451511 genes displayed around the current focus.

Configured flank5 upstream / downstreamWindow size loaded from config.ini.

Annotation sourceGCF_040545925.gff.gzResolved as <gff_root_dir>/<genome_id>/<genome_id>.gff.gz when available.

View modeGene-centered orderThis track keeps the current gene in the middle of the context window when possible.

Gene-centered contextFive upstream and five downstream genes can be shown when the configured flank count is set to 5.

Current geneHKRROther P2CSOutside P2CS

ABID56_RS04490ABID56_RS04490

ABID56_RS04495ABID56_RS04495

ABID56_RS04500ABID56_RS04500

ABID56_RS04505ABID56_RS04505

5ABID56_RS04510ABID56_RS04510

6ABID56_RS04515ABID56_RS04515

ABID56_RS04520ABID56_RS04520

ABID56_RS04525ABID56_RS04525

ABID56_RS04530ABID56_RS04530

ABID56_RS04535ABID56_RS04535

ABID56_RS04540ABID56_RS04540

Neighborhood gene cards

11 genes in the current genome window.

ABID56_RS04490ABID56_RS04490

Outside P2CS

109 567-110 970 nt · 1 404 nt · Reverse (-)

SLC13 family permease

Protein WP_354219420.1

ABID56_RS04495ABID56_RS04495

Outside P2CS

110 983-112 476 nt · 1 494 nt · Reverse (-)

tripartite tricarboxylate transporter permease

Protein WP_354219421.1

ABID56_RS04500ABID56_RS04500

Outside P2CS

112 489-112 947 nt · 459 nt · Reverse (-)

tripartite tricarboxylate transporter TctB family protein

Protein WP_354219422.1

ABID56_RS04505ABID56_RS04505

Outside P2CS

113 024-114 088 nt · 1 065 nt · Reverse (-)

tripartite tricarboxylate transporter substrate binding protein

Protein WP_354219423.1

ABID56_RS04510ABID56_RS04510

RRunclassified

114 261-114 941 nt · 681 nt · Reverse (-)

response regulator

Protein WP_354219424.1Response regulator, unclassified

ABID56_RS04515ABID56_RS04515

HKClassicCurrent focus

114 944-116 533 nt · 1 590 nt · Reverse (-)

sensor histidine kinase

Protein WP_354219425.1Probable incomplete histidine kinase

ABID56_RS04520ABID56_RS04520

Outside P2CS

116 764-117 855 nt · 1 092 nt · Forward (+)

carbohydrate kinase

Protein WP_354219426.1

ABID56_RS04525ABID56_RS04525

Outside P2CS

117 857-118 765 nt · 909 nt · Forward (+)

pseudouridine-5'-phosphate glycosidase

Protein WP_354219427.1

ABID56_RS04530ABID56_RS04530

Outside P2CS

118 804-119 055 nt · 252 nt · Reverse (-)

hypothetical protein

Protein WP_354219428.1

ABID56_RS04535ABID56_RS04535

Outside P2CS

119 124-120 197 nt · 1 074 nt · Reverse (-)

alanine racemase

Protein WP_354219429.1

ABID56_RS04540ABID56_RS04540

Outside P2CS

120 380-121 639 nt · 1 260 nt · Reverse (-)

YeeE/YedE family protein

Protein WP_354219430.1

3D Structure

Clusters

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

Available memberships1 cluster

IHKOC_451327IHK

IHKOC clustering2 sequencesid 100%cov 80%

PFAM HisKA_LIKE9 + HisKA_LIKE9

Representative GCF_042679545#ACFQ3O_RS03870

Selected clusterIHKOC_451327IHKOC clustering · IHK · 2 sequences

Representative sequenceGCF_042679545#ACFQ3O_RS03870Use this link to inspect the representative gene detail.

PFAM architectureHisKA_LIKE9 + HisKA_LIKE92 domains in the representative PFAM annotation.

Open in cluster search Open representative gene

PFAM architecture for IHKOC_451327

Simplified PFAM architecture for IHKOC_451327

PFAM domain coverage: 101 / 529 aa (19.1%)

1 aa529 aa

HisKA_LIKE9HisKA_LIKE9

Simplified architecture: HisKA_LIKE9 + HisKA_LIKE9
Raw architecture: HisKA_LIKE9[31-64] | HisKA_LIKE9[331-397]
Domain count: 2
Matched identifier: IHKOC_451327
Positioned domains: HisKA_LIKE9 31-64 ; HisKA_LIKE9 331-397

Cluster members and taxonomy

Representative gene: GCF_042679545#ACFQ3O_RS03870

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

Taxonomy Sankey will load when this section is visible.

Genome taxonomy

Alkalibacillus flavidus

Taxonomy recordAlkalibacillus flavidusTaxon ID 546 021 · GCF_040545925

AssemblyASM4054592v1 · Contigreference genome · haploid

Genome composition2 507 785 bp · 40,5% GCGenome size and GC content from the linked genome record.

Signal transduction countsGenes 26 · HK 12 · RR 14CheA 1 · PP 0

Ranked taxonomy7 ranked levels available

SuperkingdomBacteriaKingdomBacillatiPhylumBacillotaClassBacilliOrderBacillalesFamilyBacillaceaeGenusAlkalibacillus

Lineage path1 lineage nodes

1Unknown

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

Related genes

Preview from the same derived genome key