1 PilJ#1
35-128 aa · 94 aa · 15.7% of protein
Raw token
PilJ:35:0.00000000538:128:112:112P2CS-Web
Two-component systems, rebuilt for exploration
Gene detail
SSON_RS10885
Histidine kinase, Classic
Shigella sonnei Ss046 · GCF_000092525
ClassHKTypeClassicLength598 aaTM0ValidatedNoCompleteYesContextpaired
Gene IDGCF_000092525#SSON_RS10885Stable P2CS identifier used across views.
GenomeGCF_000092525Bacteria; Pseudomonadati; Pseudomonadota; Gammaproteobacteria; Enterobacterales; Enterobacteriaceae; Shigella
Domain signature
Compact overview inferred from the domain field
PilJHAMPHisKA_3HATPase_c
Protein length598 aaLength used to scale native and Biotite-like views.
Annotated domains44 with usable coordinates.
Domain coverage314 / 598 aa (52.5%)Merged over positioned domains only.
Domain description1 PilJ,1 HAMP,1 HisKA_3,1 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 aa598 aa
Domain-by-domain annotation4 items
2 HAMP#2
158-225 aa · 68 aa · 11.4% of protein
Raw token
HAMP:158:0.0000000000637:225:69:693 HisKA_3#3
390-453 aa · 64 aa · 10.7% of protein
Raw token
HisKA_3:390:2.66e-17:453:64:684 HATPase_c#4
496-583 aa · 88 aa · 14.7% of protein
Raw token
HATPase_c:496:4.4e-20:583:103:109- Raw architecture: PilJ:35:0.00000000538:128:112:112#HAMP:158:0.0000000000637:225:69:69#HisKA_3:390:2.66e-17:453:64:68#HATPase_c:496:4.4e-20:583:103:109
- Domain description: 1 PilJ,1 HAMP,1 HisKA_3,1 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::G00013
Group size22 locus tags listed below.
HK / RR1 / 1Counts resolved for the local TCS neighborhood.
Context span2057139-2059578Genomic interval covered by the local TCS group.
Identifiers
Old locus tagSSO_1955%2CSSON_1955RefSeq proteinWP_000918031.1
Context group ID
GCF_000092525::NC_007384.1::G00013Context members
SSON_RS10885SSON_RS10890
Partner locus tags
SSON_RS10885SSON_RS10890
Partner old locus tags
SSO_1955%2CSSON_1955SSO_1956%2CSSON_1956
Partner protein IDs
External references
Resolved via p2cs_annexes.db when the RefSeq protein is present in the annex table
RefSeqWP_000918031.1Primary protein accession used for annex mappings.
UniProt accessionQ3Z0U0Primary UniProt accession resolved in the annex database.
UniProt IDQ3Z0U0_SHISSDisplay identifier provided by UniProt.
GO / PubMed5 / 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_RS10885Primary locus identifier stored in the genes table.
Old locus tagSSO_1955%2CSSON_1955Legacy locus tag recovered from the local context mapping.
Contig / repliconNC_007384.1Sequence record reported by the local genomic context database.
Genomic interval2 057 139-2 058 935 nt1 797 nt · Forward (+)
StrandForward (+)Strand sign follows the local context database convention.
Local TCS group span2 057 139-2 059 578 ntGCF_000092525::NC_007384.1::G00013
Quick actions
Local neighborhood
Graphical neighborhood resolved from the local TCS context group on the current contig
GCF_000092525::NC_007384.1::G00013Graphic 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 057 139-2 059 578 nt2 440 nt
Members21 current focus gene
Local TCS group mapArrow direction follows strand. The current gene is highlighted with a stronger outline.
2 057 139 nt2 059 578 nt
Neighborhood gene cards
2 genes in the current local neighborhood.
SSON_RS10885GCF_000092525#SSON_RS10885
HKClassicCurrent focus
2 057 139-2 058 935 nt · Forward (+)
SSON_RS10890GCF_000092525#SSON_RS10890
RRNarL
2 058 928-2 059 578 nt · Forward (+)
Clusters
CD-HIT memberships and selected cluster details for the current gene class
Available memberships1 cluster
Representative sequenceGCF_000092525#SSON_RS10885The current gene is the representative for this cluster.
PFAM architecturePilJ + HAMP + HisKA_3 + HATPase_c4 domains in the representative PFAM annotation.
PFAM architecture for HKOC_1061582
Simplified PFAM architecture for HKOC_1061582
PFAM domain coverage: 301 / 598 aa (50.3%)
1 aa598 aa
PilJHAMPHisKA_3HATPase_c
- Simplified architecture: PilJ + HAMP + HisKA_3 + HATPase_c
- Raw architecture: PilJ[35-129] | HAMP[173-224] | HisKA_3[390-453] | HATPase_c[496-585]
- Domain count: 4
- Matched identifier: HKOC_1061582
- Positioned domains: PilJ 35-129 ; HAMP 173-224 ; HisKA_3 390-453 ; HATPase_c 496-585
Cluster members and taxonomy
Representative gene: GCF_000092525#SSON_RS10885
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