1 HAMP#1
267-335 aa · 69 aa · 10.4% of protein
Raw token
HAMP:267:0.00000000000000107:335:69:69P2CS-Web
Two-component systems, rebuilt for exploration
Gene detail
HMPREF0175_RS05560
Histidine kinase, Classic
Bifidobacterium longum subsp. longum ATCC 55813 · GCF_000003135
ClassHKTypeClassicLength663 aaTM0ValidatedNoCompleteYesContextpaired
Gene IDGCF_000003135#HMPREF0175_RS05560Stable P2CS identifier used across views.
Domain signature
Compact overview inferred from the domain field
HAMPHisKAHATPase_c
Protein length663 aaLength used to scale native and Biotite-like views.
Annotated domains33 with usable coordinates.
Domain coverage287 / 663 aa (43.3%)Merged over positioned domains only.
Domain description1 HAMP,1 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
Native P2CS viewFrontend rendering from the parsed domain string and TMPRED protein features.
1 aa663 aa
Domain-by-domain annotation3 items
2 HisKA#2
347-416 aa · 70 aa · 10.6% of protein
Raw token
HisKA:347:2.64e-17:416:70:643 HATPase_c#3
480-627 aa · 148 aa · 22.3% of protein
Raw token
HATPase_c:480:3.62e-21:627:148:109- Raw architecture: HAMP:267:0.00000000000000107:335:69:69#HisKA:347:2.64e-17:416:70:64#HATPase_c:480:3.62e-21:627:148:109
- Domain description: 1 HAMP,1 HisKA,1 HATPase_c
- TM description: N/A
- TMPRED source: No TMPRED file loaded
- TMPRED segments: N/A
- Complete: Yes
Protein sequence
On-demand local amino-acid sequence in FASTA format
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
Context labelpairedGCF_000003135::NZ_GG666850.1::G00007
Group size22 locus tags listed below.
HK / RR1 / 1Counts resolved for the local TCS neighborhood.
Context span365325-368078Genomic interval covered by the local TCS group.
Identifiers
Old locus tagHMPREF0175_1156RefSeq proteinWP_032746891.1
Context group ID
GCF_000003135::NZ_GG666850.1::G00007Context members
HMPREF0175_RS05565HMPREF0175_RS05560
Partner locus tags
HMPREF0175_RS05565HMPREF0175_RS05560
Partner old locus tags
HMPREF0175_1155HMPREF0175_1156
Partner protein IDs
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_032746891.1.
Genomic coordinates
Resolved via p2cs_tcs_context.db when the current locus tag is present in the local context table
Current locus tagHMPREF0175_RS05560Primary locus identifier stored in the genes table.
Old locus tagHMPREF0175_1156Legacy locus tag recovered from the local context mapping.
Contig / repliconNZ_GG666850.1Sequence record reported by the local genomic context database.
Genomic interval366 087-368 078 nt1 992 nt · Forward (+)
StrandForward (+)Strand sign follows the local context database convention.
Local TCS group span365 325-368 078 ntGCF_000003135::NZ_GG666850.1::G00007
Quick actions
Genome neighborhood
Gene-centered window parsed directly from the configured gzipped GFF annotation
GCF_000003135 · NZ_GG666850.1Graphic view
Compact keeps a quick overview. Biotite-like switches to a coordinate-aware biological layout with strand and zoom.
Centered locusHMPREF0175_RS0556011 genes displayed around the current focus.
Configured flank5 upstream / downstreamWindow size loaded from config.ini.
Annotation sourceGCF_000003135.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
1
HMPREF0175_RS05580HMPREF0175_RS05580
2
HMPREF0175_RS05575groL
3
HMPREF0175_RS05570HMPREF0175_RS05570
4
HMPREF0175_RS0109810HMPREF0175_RS0109810
7
HMPREF0175_RS05555HMPREF0175_RS05555
8
HMPREF0175_RS05550HMPREF0175_RS05550
9
HMPREF0175_RS05545HMPREF0175_RS05545
10
HMPREF0175_RS05540HMPREF0175_RS05540
11
HMPREF0175_RS05535HMPREF0175_RS05535
Neighborhood gene cards
11 genes in the current genome window.
HMPREF0175_RS05580HMPREF0175_RS05580
Outside P2CS
361 962-362 201 nt · 240 nt · Forward (+)
cold-shock protein
HMPREF0175_RS05575groL
Outside P2CS
362 439-364 064 nt · 1 626 nt · Forward (+)
chaperonin GroEL
HMPREF0175_RS05570HMPREF0175_RS05570
Outside P2CS
364 161-364 451 nt · 291 nt · Reverse (-)
WXG100 family type VII secretion target
HMPREF0175_RS0109810HMPREF0175_RS0109810
Outside P2CS
364 667-365 332 nt · 666 nt · Forward (+)
TPM domain-containing protein
HMPREF0175_RS05565HMPREF0175_RS05565
RROmpR
365 325-366 056 nt · 732 nt · Forward (+)
response regulator transcription factor
HMPREF0175_RS05560HMPREF0175_RS05560
HKClassicCurrent focus
366 087-368 078 nt · 1 992 nt · Forward (+)
HAMP domain-containing sensor histidine kinase
HMPREF0175_RS05555HMPREF0175_RS05555
Outside P2CS
368 148-368 537 nt · 390 nt · Forward (+)
cold-shock protein
HMPREF0175_RS05550HMPREF0175_RS05550
Outside P2CS
368 546-369 733 nt · 1 188 nt · Forward (+)
DUF3027 domain-containing protein
HMPREF0175_RS05545HMPREF0175_RS05545
Outside P2CS
369 845-370 810 nt · 966 nt · Reverse (-)
universal stress protein
HMPREF0175_RS05540HMPREF0175_RS05540
Outside P2CS
370 960-373 569 nt · 2 610 nt · Forward (+)
ATP-dependent Clp protease ATP-binding subunit
HMPREF0175_RS05535HMPREF0175_RS05535
Outside P2CS
373 749-375 068 nt · 1 320 nt · Reverse (-)
amidohydrolase family protein
3D Structure
No local structure root: /mnt/p2cs-s3/P2CS_WEB/DATAS/SP_CIF
No local CIF or PDB file was detected for this record.
No CIF or PDB file was found for HKOC_0864147 under /home/biam/MYTOOLS/p2cs-web/DATAS/MassiveFold/work/recovered_by_cluster_all_ranked/clusters.
No UniProt accession is available for this gene.
Clusters
CD-HIT memberships and selected cluster details for the current gene class
Available memberships1 cluster
Representative sequenceGCF_000003135#HMPREF0175_RS05560The current gene is the representative for this cluster.
PFAM architectureHAMP + HisKA + HATPase_c3 domains in the representative PFAM annotation.
PFAM architecture for HKOC_0864147
Simplified PFAM architecture for HKOC_0864147
PFAM domain coverage: 268 / 663 aa (40.4%)
1 aa663 aa
HAMPHisKAHATPase_c
- Simplified architecture: HAMP + HisKA + HATPase_c
- Raw architecture: HAMP[284-335] | HisKA[348-416] | HATPase_c[480-626]
- Domain count: 3
- Matched identifier: HKOC_0864147
- Positioned domains: HAMP 284-335 ; HisKA 348-416 ; HATPase_c 480-626
Cluster members and taxonomy
Representative gene: GCF_000003135#HMPREF0175_RS05560
Sankey plot built from the taxonomy of all members in the selected cluster.
Genome taxonomy
Bifidobacterium longum subsp. longum ATCC 55813
Taxonomy recordBifidobacterium longum subsp. longum ATCC 55813Taxon ID 548 480 · GCF_000003135
AssemblyASM313v1 · Scaffoldhaploid
Genome composition2 396 359 bp · 60,5% GCGenome size and GC content from the linked genome record.
Signal transduction countsGenes 20 · HK 10 · RR 10CheA 0 · PP 0
Ranked taxonomy7 ranked levels available
SuperkingdomBacteriaKingdomBacillatiPhylumActinomycetotaClassActinomycetesOrderBifidobacterialesFamilyBifidobacteriaceaeGenusBifidobacterium
Lineage path1 lineage nodes
1Unknown
Related genes
Preview from the same derived genome key