1 HAMP#1
192-259 aa · 68 aa · 11.2% of protein
Raw token
HAMP:192:0.0000000144:259:69:69P2CS-Web
Two-component systems, rebuilt for exploration
Gene detail
SSON_RS12665
Histidine kinase, Classic
Shigella sonnei Ss046 · GCF_000092525
ClassHKTypeClassicLength608 aaTM0ValidatedNoCompleteYesContextpaired
Gene IDGCF_000092525#SSON_RS12665Stable P2CS identifier used across views.
GenomeGCF_000092525Bacteria; Pseudomonadati; Pseudomonadota; Gammaproteobacteria; Enterobacterales; Enterobacteriaceae; Shigella
Domain signature
Compact overview inferred from the domain field
HAMPPASHisKAHATPase_c
Protein length608 aaLength used to scale native and Biotite-like views.
Annotated domains44 with usable coordinates.
Domain coverage346 / 608 aa (56.9%)Merged over positioned domains only.
Domain description1 HAMP,1 PAS,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 aa608 aa
Domain-by-domain annotation4 items
2 PAS#2
265-370 aa · 106 aa · 17.4% of protein
Raw token
PAS:265:4.45e-21:370:110:1133 HisKA#3
389-452 aa · 64 aa · 10.5% of protein
Raw token
HisKA:389:0.00000000000000207:452:64:644 HATPase_c#4
495-602 aa · 108 aa · 17.8% of protein
Raw token
HATPase_c:495:4.84e-27:602:112:109- Raw architecture: HAMP:192:0.0000000144:259:69:69#PAS:265:4.45e-21:370:110:113#HisKA:389:0.00000000000000207:452:64:64#HATPase_c:495:4.84e-27:602:112:109
- Domain description: 1 HAMP,1 PAS,1 HisKA,1 HATPase_c
- 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 labelpairedGCF_000092525::NC_007384.1::G00020
Group size22 locus tags listed below.
HK / RR1 / 1Counts resolved for the local TCS neighborhood.
Context span2395016-2398224Genomic interval covered by the local TCS group.
Identifiers
Old locus tagSSO_2278%2CSSON_2278RefSeq proteinWP_000559122.1
Context group ID
GCF_000092525::NC_007384.1::G00020Context members
SSON_RS12665SSON_RS12670
Partner locus tags
SSON_RS12665SSON_RS12670
Partner old locus tags
SSO_2278%2CSSON_2278SSO_2279%2CSSON_2279
Partner protein IDs
External references
Resolved via p2cs_annexes.db when the RefSeq protein is present in the annex table
RefSeqWP_000559122.1Primary protein accession used for annex mappings.
UniProt accessionQ3YZY7Primary UniProt accession resolved in the annex database.
UniProt IDQ3YZY7_SHISSDisplay identifier provided by UniProt.
GO / PubMed4 / 1Unique GO terms and literature references available below.
Reference hubs
PubMed
Genomic coordinates
Resolved via p2cs_tcs_context.db when the current locus tag is present in the local context table
Current locus tagSSON_RS12665Primary locus identifier stored in the genes table.
Old locus tagSSO_2278%2CSSON_2278Legacy locus tag recovered from the local context mapping.
Contig / repliconNC_007384.1Sequence record reported by the local genomic context database.
Genomic interval2 395 016-2 396 842 nt1 827 nt · Forward (+)
StrandForward (+)Strand sign follows the local context database convention.
Local TCS group span2 395 016-2 398 224 ntGCF_000092525::NC_007384.1::G00020
Quick actions
Local neighborhood
Graphical neighborhood resolved from the local TCS context group on the current contig
GCF_000092525::NC_007384.1::G00020Graphic view
Compact keeps a quick overview. Biotite-like switches to a coordinate-aware biological layout with strand and zoom.
Context labelpairedNeighborhood members are ordered by genomic coordinates.
Contig / repliconNC_007384.1All displayed genes belong to this local TCS context.
Neighborhood span2 395 016-2 398 224 nt3 209 nt
Members21 current focus gene
Local TCS group mapArrow direction follows strand. The current gene is highlighted with a stronger outline.
2 395 016 nt2 398 224 nt
Neighborhood gene cards
2 genes in the current local neighborhood.
SSON_RS12665GCF_000092525#SSON_RS12665
HKClassicCurrent focus
2 395 016-2 396 842 nt · Forward (+)
SSON_RS12670GCF_000092525#SSON_RS12670
RRPrrA
2 396 839-2 398 224 nt · Forward (+)
Clusters
CD-HIT memberships and selected cluster details for the current gene class
Available memberships1 cluster
Representative sequenceGCF_000092525#SSON_RS12665The current gene is the representative for this cluster.
PFAM architecturePAS + HisKA + HATPase_c3 domains in the representative PFAM annotation.
PFAM architecture for HKOC_1013012
Simplified PFAM architecture for HKOC_1013012
PFAM domain coverage: 273 / 608 aa (44.9%)
1 aa608 aa
PASHisKAHATPase_c
- Simplified architecture: PAS + HisKA + HATPase_c
- Raw architecture: PAS[265-369] | HisKA[389-451] | HATPase_c[496-600]
- Domain count: 3
- Matched identifier: HKOC_1013012
- Positioned domains: PAS 265-369 ; HisKA 389-451 ; HATPase_c 496-600
Cluster members and taxonomy
Representative gene: GCF_000092525#SSON_RS12665
Sankey plot built from the taxonomy of all members in the selected cluster.
Genome taxonomy
Unknown
Taxonomy recordUnknownTaxon ID 300 269 · GCF_000092525
AssemblyASM9252v1 · Complete Genomehaploid
Genome composition5 055 316 bp · 51,0% GCShigella sonnei Ss046
Signal transduction countsGenes 60 · HK 29 · RR 31CheA 1 · PP 0
Ranked taxonomy7 ranked levels available
SuperkingdomBacteriaKingdomPseudomonadatiPhylumPseudomonadotaClassGammaproteobacteriaOrderEnterobacteralesFamilyEnterobacteriaceaeGenusShigella
Lineage path7 lineage nodes
1Bacteria2Pseudomonadati3Pseudomonadota4Gammaproteobacteria5Enterobacterales6Enterobacteriaceae7Shigella
Related genes
Preview from the same derived genome key