1 HAMP#1
188-257 aa · 70 aa · 14.6% of protein
Raw token
HAMP:188:0.0000000000682:257:71:69P2CS-Web
Two-component systems, rebuilt for exploration
Gene detail
SFV_RS02780
Histidine kinase, Classic
Shigella flexneri 5 str. 8401 · GCF_000013585
ClassHKTypeClassicLength480 aaTM0ValidatedNoCompleteYesContextpaired
Gene IDGCF_000013585#SFV_RS02780Stable 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 length480 aaLength used to scale native and Biotite-like views.
Annotated domains33 with usable coordinates.
Domain coverage246 / 480 aa (51.2%)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 aa480 aa
Domain-by-domain annotation3 items
2 HisKA#2
261-327 aa · 67 aa · 14.0% of protein
Raw token
HisKA:261:0.00000000000139:327:67:643 HATPase_c#3
371-479 aa · 109 aa · 22.7% of protein
Raw token
HATPase_c:371:2.1e-29:479:110:109- Raw architecture: HAMP:188:0.0000000000682:257:71:69#HisKA:261:0.00000000000139:327:67:64#HATPase_c:371:2.1e-29:479:110:109
- 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::G00003
Group size22 locus tags listed below.
HK / RR1 / 1Counts resolved for the local TCS neighborhood.
Context span528781-530896Genomic interval covered by the local TCS group.
Identifiers
Old locus tagSFV_0503RefSeq proteinWP_000253804.1
Context group ID
GCF_000013585::NC_008258.1::G00003Context members
SFV_RS02780SFV_RS02785
Partner locus tags
SFV_RS02780SFV_RS02785
Partner old locus tags
SFV_0503SFV_0504
Partner protein IDs
External references
Resolved via p2cs_annexes.db when the RefSeq protein is present in the annex table
RefSeqWP_000253804.1Primary protein accession used for annex mappings.
UniProt accessionQ0T762Primary UniProt accession resolved in the annex database.
UniProt IDQ0T762_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_RS02780Primary locus identifier stored in the genes table.
Old locus tagSFV_0503Legacy locus tag recovered from the local context mapping.
Contig / repliconNC_008258.1Sequence record reported by the local genomic context database.
Genomic interval528 781-530 223 nt1 443 nt · Reverse (-)
StrandReverse (-)Strand sign follows the local context database convention.
Local TCS group span528 781-530 896 ntGCF_000013585::NC_008258.1::G00003
Quick actions
Local neighborhood
Graphical neighborhood resolved from the local TCS context group on the current contig
GCF_000013585::NC_008258.1::G00003Graphic 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 span528 781-530 896 nt2 116 nt
Members21 current focus gene
Local TCS group mapArrow direction follows strand. The current gene is highlighted with a stronger outline.
528 781 nt530 896 nt
Neighborhood gene cards
2 genes in the current local neighborhood.
SFV_RS02780GCF_000013585#SFV_RS02780
HKClassicCurrent focus
528 781-530 223 nt · Reverse (-)
SFV_RS02785GCF_000013585#SFV_RS02785
RROmpR
530 213-530 896 nt · Reverse (-)
Clusters
CD-HIT memberships and selected cluster details for the current gene class
Available memberships1 cluster
Representative sequenceGCF_000013585#SFV_RS02780The current gene is the representative for this cluster.
PFAM architectureCusS + HAMP + HisKA + HATPase_c4 domains in the representative PFAM annotation.
PFAM architecture for HKOC_1619022
Simplified PFAM architecture for HKOC_1619022
PFAM domain coverage: 395 / 480 aa (82.3%)
1 aa480 aa
CusSHAMPHisKAHATPase_c
- Simplified architecture: CusS + HAMP + HisKA + HATPase_c
- Raw architecture: CusS[8-180] | HAMP[210-257] | HisKA[262-326] | HATPase_c[371-479]
- Domain count: 4
- Matched identifier: HKOC_1619022
- Positioned domains: CusS 8-180 ; HAMP 210-257 ; HisKA 262-326 ; HATPase_c 371-479
Cluster members and taxonomy
Representative gene: GCF_000013585#SFV_RS02780
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