Gene detail

SSON_RS13715

Histidine kinase, Unorthodox

Shigella sonnei Ss046 · GCF_000092525

Open genome Open selected cluster RefSeq UniProt

ClassHKTypeUnorthodoxLength1197 aaTM0ValidatedNoCompleteYesContextpaired

Gene IDGCF_000092525#SSON_RS13715Stable P2CS identifier used across views.

GenomeGCF_000092525Bacteria; Pseudomonadati; Pseudomonadota; Gammaproteobacteria; Enterobacterales; Enterobacteriaceae; Shigella

Selected clusterHKOC_0161026Run 6 · 1322 sequences · id 100% · cov 80% · representative

External referencesWP_005150262.1 · Q3YZG0 · MIST4 SSON_RS13715RefSeq · UniProt · MIST4

Domain signature

Compact overview inferred from the domain field

PBPbHisKAHATPase_cResponse_regHpt

Protein length1197 aaLength used to scale native and Biotite-like views.

Annotated domains66 with usable coordinates.

Domain coverage796 / 1197 aa (66.5%)Merged over positioned domains only.

Domain description2 PBPb,1 HisKA,1 HATPase_c,1 Response_reg,1 HptSummary 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

Domain view

Native Biotite-like

Native P2CS viewFrontend rendering from the parsed domain string and TMPRED protein features.

1 aa1197 aa

Domain-by-domain annotation6 items

1 PBPb#1

73-276 aa · 204 aa · 17.0% of protein

Raw tokenPBPb:73:0.00000000000000805:276:209:219

2 PBPb#2

304-519 aa · 216 aa · 18.0% of protein

Raw tokenPBPb:304:1.75e-39:519:223:219

3 HisKA#3

711-777 aa · 67 aa · 5.6% of protein

Raw tokenHisKA:711:1.62e-16:777:67:64

4 HATPase_c#4

825-938 aa · 114 aa · 9.5% of protein

Raw tokenHATPase_c:825:2.25e-32:938:114:109

5 Response_reg#5

961-1070 aa · 110 aa · 9.2% of protein

Raw tokenResponse_reg:961:1.93e-39:1070:110:111

6 Hpt#6

1104-1188 aa · 85 aa · 7.1% of protein

Raw tokenHpt:1104:0.000000101:1188:85:84

Raw architecture: PBPb:73:0.00000000000000805:276:209:219#PBPb:304:1.75e-39:519:223:219#HisKA:711:1.62e-16:777:67:64#HATPase_c:825:2.25e-32:938:114:109#Response_reg:961:1.93e-39:1070:110:111#Hpt:1104:0.000000101:1188:85:84
Domain description: 2 PBPb,1 HisKA,1 HATPase_c,1 Response_reg,1 Hpt
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::G00021

Group size22 locus tags listed below.

HK / RR1 / 1Counts resolved for the local TCS neighborhood.

Context span2596923-2601135Genomic interval covered by the local TCS group.

Identifiers

Old locus tagSSO_2461%2CSSON_2461RefSeq proteinWP_005150262.1

Context group IDGCF_000092525::NC_007384.1::G00021

Context members

SSON_RS13710SSON_RS13715

Partner locus tags

SSON_RS13710SSON_RS13715

Partner old locus tags

SSO_2460%2CSSON_2460SSO_2461%2CSSON_2461

Partner protein IDs

WP_000991366.1 WP_005150262.1

External references

Resolved via p2cs_annexes.db when the RefSeq protein is present in the annex table

RefSeqWP_005150262.1Primary protein accession used for annex mappings.

UniProt accessionQ3YZG0Primary UniProt accession resolved in the annex database.

UniProt IDQ3YZG0_SHISSDisplay identifier provided by UniProt.

GO / PubMed4 / 1Unique GO terms and literature references available below.

Reference hubs

Open RefSeq Open UniProt accession

GO terms

GO:0005886 GO:0005524 GO:0009927 GO:0000155

PubMed

16275786

Genomic coordinates

Resolved via p2cs_tcs_context.db when the current locus tag is present in the local context table

Current locus tagSSON_RS13715Primary locus identifier stored in the genes table.

Old locus tagSSO_2461%2CSSON_2461Legacy locus tag recovered from the local context mapping.

Contig / repliconNC_007384.1Sequence record reported by the local genomic context database.

Genomic interval2 597 542-2 601 135 nt3 594 nt · Forward (+)

StrandForward (+)Strand sign follows the local context database convention.

Local TCS group span2 596 923-2 601 135 ntGCF_000092525::NC_007384.1::G00021

Quick actions

Open genome Search genes in genome

Local neighborhood

Graphical neighborhood resolved from the local TCS context group on the current contig

GCF_000092525::NC_007384.1::G00021

Graphic view

Compact Biotite-like

Zoom

Full window Focus gene

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 596 923-2 601 135 nt4 213 nt

Members21 current focus gene

Local TCS group mapArrow direction follows strand. The current gene is highlighted with a stronger outline.

2 596 923 nt2 601 135 nt

+-SSON_RS13710 SSON_RS13715

Neighborhood gene cards

2 genes in the current local neighborhood.

SSON_RS13710GCF_000092525#SSON_RS13710

RRunclassified

2 596 923-2 597 537 nt · Forward (+)

Old locus SSO_2460%2CSSON_2460RefSeq WP_000991366.1

Open gene

SSON_RS13715GCF_000092525#SSON_RS13715

HKUnorthodoxCurrent focus

2 597 542-2 601 135 nt · Forward (+)

Old locus SSO_2461%2CSSON_2461RefSeq WP_005150262.1

Open current gene

Clusters

CD-HIT memberships and selected cluster details for the current gene class

Available memberships1 cluster

HKOC_0161026HK

Run 61322 sequencesid 100%cov 80%

PFAM SBP_bac_3 + SBP_bac_3 + HisKA + HATPase_c + Response_reg + Hpt

Current gene is the representative sequence.

Selected clusterHKOC_0161026Run 6 · HK · 1322 sequences

Representative sequenceGCF_000092525#SSON_RS13715The current gene is the representative for this cluster.

PFAM architectureSBP_bac_3 + SBP_bac_3 + HisKA + HATPase_c + Response_reg + Hpt6 domains in the representative PFAM annotation.

Open in cluster search

PFAM architecture for HKOC_0161026

Simplified PFAM architecture for HKOC_0161026

PFAM domain coverage: 802 / 1197 aa (67.0%)

1 aa1197 aa

SBP_bac_3SBP_bac_3HisKAHATPase_cResponse_regHpt

Simplified architecture: SBP_bac_3 + SBP_bac_3 + HisKA + HATPase_c + Response_reg + Hpt
Raw architecture: SBP_bac_3[63-276] | SBP_bac_3[306-520] | HisKA[711-777] | HATPase_c[825-937] | Response_reg[961-1070] | Hpt[1104-1186]
Domain count: 6
Matched identifier: HKOC_0161026
Positioned domains: SBP_bac_3 63-276 ; SBP_bac_3 306-520 ; HisKA 711-777 ; HATPase_c 825-937 ; Response_reg 961-1070 ; Hpt 1104-1186

Cluster members and taxonomy

Representative gene: GCF_000092525#SSON_RS13715

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

Open genome Search genes in genome Search HK genes NCBI assembly files

Related genes

Preview from the same derived genome key