1 KdpD#1
21-230 aa · 210 aa · 23.5% of protein
Raw token
KdpD:21:4.58e-143:230:210:210P2CS-Web
Two-component systems, rebuilt for exploration
Gene detail
SSON_RS03445
Histidine kinase, Classic
Shigella sonnei Ss046 · GCF_000092525
ClassHKTypeClassicLength894 aaTM0ValidatedNoCompleteYesContextpaired
Gene IDGCF_000092525#SSON_RS03445Stable P2CS identifier used across views.
GenomeGCF_000092525Bacteria; Pseudomonadati; Pseudomonadota; Gammaproteobacteria; Enterobacterales; Enterobacteriaceae; Shigella
Domain signature
Compact overview inferred from the domain field
KdpDGAF_3HisKAHATPase_c
Protein length894 aaLength used to scale native and Biotite-like views.
Annotated domains44 with usable coordinates.
Domain coverage502 / 894 aa (56.2%)Merged over positioned domains only.
Domain description1 KdpD,1 GAF_3,1 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 aa894 aa
Domain-by-domain annotation4 items
2 GAF_3#2
527-644 aa · 118 aa · 13.2% of protein
Raw token
GAF_3:527:0.00000000000393:644:130:1293 HisKA#3
664-730 aa · 67 aa · 7.5% of protein
Raw token
HisKA:664:0.000000000000264:730:68:644 HATPase_c#4
774-880 aa · 107 aa · 12.0% of protein
Raw token
HATPase_c:774:1.14e-30:880:107:109- Raw architecture: KdpD:21:4.58e-143:230:210:210#GAF_3:527:0.00000000000393:644:130:129#HisKA:664:0.000000000000264:730:68:64#HATPase_c:774:1.14e-30:880:107:109
- Domain description: 1 KdpD,1 GAF_3,1 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::G00004
Group size22 locus tags listed below.
HK / RR1 / 1Counts resolved for the local TCS neighborhood.
Context span682397-685755Genomic interval covered by the local TCS group.
Identifiers
Old locus tagSSO_0646%2CSSON_0646RefSeq proteinWP_005145234.1
Context group ID
GCF_000092525::NC_007384.1::G00004Context members
SSON_RS03440SSON_RS03445
Partner locus tags
SSON_RS03440SSON_RS03445
Partner old locus tags
SSO_0645%2CSSON_0645SSO_0646%2CSSON_0646
Partner protein IDs
External references
Resolved via p2cs_annexes.db when the RefSeq protein is present in the annex table
RefSeqWP_005145234.1Primary protein accession used for annex mappings.
UniProt accessionQ3Z4A8Primary UniProt accession resolved in the annex database.
UniProt IDQ3Z4A8_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_RS03445Primary locus identifier stored in the genes table.
Old locus tagSSO_0646%2CSSON_0646Legacy locus tag recovered from the local context mapping.
Contig / repliconNC_007384.1Sequence record reported by the local genomic context database.
Genomic interval683 071-685 755 nt2 685 nt · Reverse (-)
StrandReverse (-)Strand sign follows the local context database convention.
Local TCS group span682 397-685 755 ntGCF_000092525::NC_007384.1::G00004
Quick actions
Local neighborhood
Graphical neighborhood resolved from the local TCS context group on the current contig
GCF_000092525::NC_007384.1::G00004Graphic 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 span682 397-685 755 nt3 359 nt
Members21 current focus gene
Local TCS group mapArrow direction follows strand. The current gene is highlighted with a stronger outline.
682 397 nt685 755 nt
Neighborhood gene cards
2 genes in the current local neighborhood.
SSON_RS03440GCF_000092525#SSON_RS03440
RROmpR
682 397-683 074 nt · Reverse (-)
SSON_RS03445GCF_000092525#SSON_RS03445
HKClassicCurrent focus
683 071-685 755 nt · Reverse (-)
Clusters
CD-HIT memberships and selected cluster details for the current gene class
Available memberships1 cluster
Representative sequenceGCF_000092525#SSON_RS03445The current gene is the representative for this cluster.
PFAM architectureKdpD + DUF4118 + GAF_3 + HisKA + HATPase_c5 domains in the representative PFAM annotation.
PFAM architecture for HKOC_0419574
Simplified PFAM architecture for HKOC_0419574
PFAM domain coverage: 607 / 894 aa (67.9%)
1 aa894 aa
KdpDDUF4118GAF_3HisKAHATPase_c
- Simplified architecture: KdpD + DUF4118 + GAF_3 + HisKA + HATPase_c
- Raw architecture: KdpD[22-230] | DUF4118[403-508] | GAF_3[527-644] | HisKA[664-730] | HATPase_c[776-882]
- Domain count: 5
- Matched identifier: HKOC_0419574
- Positioned domains: KdpD 22-230 ; DUF4118 403-508 ; GAF_3 527-644 ; HisKA 664-730 ; HATPase_c 776-882
Cluster members and taxonomy
Representative gene: GCF_000092525#SSON_RS03445
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