1 HAMP#1
164-232 aa · 69 aa · 15.4% of protein
Raw token
HAMP:164:0.00000143:232:70:69P2CS-Web
Two-component systems, rebuilt for exploration
Gene detail
SFV_RS16980
Histidine kinase, Classic
Shigella flexneri 5 str. 8401 · GCF_000013585
ClassHKTypeClassicLength449 aaTM0ValidatedNoCompleteYesContextpaired
Gene IDGCF_000013585#SFV_RS16980Stable P2CS identifier used across views.
GenomeGCF_000013585Bacteria; Pseudomonadati; Pseudomonadota; Gammaproteobacteria; Enterobacterales; Enterobacteriaceae; Shigella
Domain signature
Compact overview inferred from the domain field
HAMPHisKAHATPase_c
Protein length449 aaLength used to scale native and Biotite-like views.
Annotated domains33 with usable coordinates.
Domain coverage228 / 449 aa (50.8%)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 aa449 aa
Domain-by-domain annotation3 items
2 HisKA#2
238-301 aa · 64 aa · 14.3% of protein
Raw token
HisKA:238:0.00000000000525:301:64:643 HATPase_c#3
348-442 aa · 95 aa · 21.2% of protein
Raw token
HATPase_c:348:3.26e-25:442:99:109- Raw architecture: HAMP:164:0.00000143:232:70:69#HisKA:238:0.00000000000525:301:64:64#HATPase_c:348:3.26e-25:442:99:109
- 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
Context mapping
Resolved via p2cs_tcs_context.db when a locus tag match exists
Context labelpairedGCF_000013585::NC_008258.1::G00026
Group size22 locus tags listed below.
HK / RR1 / 1Counts resolved for the local TCS neighborhood.
Context span3136706-3138711Genomic interval covered by the local TCS group.
Identifiers
Old locus tagSFV_3072RefSeq proteinWP_000673369.1
Context group ID
GCF_000013585::NC_008258.1::G00026Context members
SFV_RS16975SFV_RS16980
Partner locus tags
SFV_RS16975SFV_RS16980
Partner old locus tags
SFV_3071SFV_3072
Partner protein IDs
External references
Resolved via p2cs_annexes.db when the RefSeq protein is present in the annex table
RefSeqWP_000673369.1Primary protein accession used for annex mappings.
UniProt accessionQ0T0N0Primary UniProt accession resolved in the annex database.
UniProt IDQ0T0N0_SHIF8Display identifier provided by UniProt.
GO / PubMed3 / 1Unique GO terms and literature references available below.
Reference hubs
GO terms
PubMed
Genomic coordinates
Resolved via p2cs_tcs_context.db when the current locus tag is present in the local context table
Current locus tagSFV_RS16980Primary locus identifier stored in the genes table.
Old locus tagSFV_3072Legacy locus tag recovered from the local context mapping.
Contig / repliconNC_008258.1Sequence record reported by the local genomic context database.
Genomic interval3 137 362-3 138 711 nt1 350 nt · Forward (+)
StrandForward (+)Strand sign follows the local context database convention.
Local TCS group span3 136 706-3 138 711 ntGCF_000013585::NC_008258.1::G00026
Quick actions
Local neighborhood
Graphical neighborhood resolved from the local TCS context group on the current contig
GCF_000013585::NC_008258.1::G00026Graphic 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_008258.1All displayed genes belong to this local TCS context.
Neighborhood span3 136 706-3 138 711 nt2 006 nt
Members21 current focus gene
Local TCS group mapArrow direction follows strand. The current gene is highlighted with a stronger outline.
3 136 706 nt3 138 711 nt
Neighborhood gene cards
2 genes in the current local neighborhood.
SFV_RS16975GCF_000013585#SFV_RS16975
RROmpR
3 136 706-3 137 365 nt · Forward (+)
SFV_RS16980GCF_000013585#SFV_RS16980
HKClassicCurrent focus
3 137 362-3 138 711 nt · Forward (+)
Clusters
CD-HIT memberships and selected cluster details for the current gene class
Available memberships1 cluster
Representative sequenceGCF_000013585#SFV_RS16980The current gene is the representative for this cluster.
PFAM architecture2CSK_N + HisKA + HATPase_c3 domains in the representative PFAM annotation.
PFAM architecture for HKOC_1973195
Simplified PFAM architecture for HKOC_1973195
PFAM domain coverage: 297 / 449 aa (66.1%)
1 aa449 aa
2CSK_NHisKAHATPase_c
- Simplified architecture: 2CSK_N + HisKA + HATPase_c
- Raw architecture: 2CSK_N[23-157] | HisKA[237-301] | HATPase_c[349-445]
- Domain count: 3
- Matched identifier: HKOC_1973195
- Positioned domains: 2CSK_N 23-157 ; HisKA 237-301 ; HATPase_c 349-445
Cluster members and taxonomy
Representative gene: GCF_000013585#SFV_RS16980
Sankey plot built from the taxonomy of all members in the selected cluster.
Genome taxonomy
Unknown
Taxonomy recordUnknownTaxon ID 373 384 · GCF_000013585
AssemblyASM1358v1 · Complete Genomehaploid
Genome composition4 574 284 bp · 51,0% GCShigella flexneri 5 str. 8401
Signal transduction countsGenes 55 · HK 25 · RR 30CheA 1 · PP 0
Ranked taxonomy7 ranked levels available
SuperkingdomBacteriaKingdomPseudomonadatiPhylumPseudomonadotaClassGammaproteobacteriaOrderEnterobacteralesFamilyEnterobacteriaceaeGenusShigella
Lineage path7 lineage nodes
1Bacteria2Pseudomonadati3Pseudomonadota4Gammaproteobacteria5Enterobacterales6Enterobacteriaceae7Shigella
Related genes
Preview from the same derived genome key