Gene detail

SFV_RS13520

Histidine kinase, Unorthodox

Shigella flexneri 5 str. 8401 · GCF_000013585

Open genome Open selected cluster RefSeq UniProt

ClassHKTypeUnorthodoxLength1197 aaTM0ValidatedNoCompleteYesContextpaired

Gene IDGCF_000013585#SFV_RS13520Stable P2CS identifier used across views.

GenomeGCF_000013585Bacteria; Pseudomonadati; Pseudomonadota; Gammaproteobacteria; Enterobacterales; Enterobacteriaceae; Shigella

Selected clusterHKOC_0161015Run 6 · 102 sequences · id 100% · cov 80% · representative

External referencesWP_005070035.1 · Q0T2C7 · MIST4 SFV_RS13520RefSeq · 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 coverage797 / 1197 aa (66.6%)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:73:0.00000000000000194:276:209:219

2 PBPb#2

303-519 aa · 217 aa · 18.1% of protein

Raw tokenPBPb:303:8.1e-40:519:224:219

3 HisKA#3

711-777 aa · 67 aa · 5.6% of protein

Raw tokenHisKA:711:1.9e-16:777:67:64

4 HATPase_c#4

825-938 aa · 114 aa · 9.5% of protein

Raw tokenHATPase_c:825:1.03e-31:938:114:109

5 Response_reg#5

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

Raw tokenResponse_reg:961:1.18e-39:1070:110:111

6 Hpt#6

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

Raw tokenHpt:1104:0.000000404:1188:85:84

Raw architecture: PBPb:73:0.00000000000000194:276:209:219#PBPb:303:8.1e-40:519:224:219#HisKA:711:1.9e-16:777:67:64#HATPase_c:825:1.03e-31:938:114:109#Response_reg:961:1.18e-39:1070:110:111#Hpt:1104:0.000000404:1188:85:84
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_000013585::NC_008258.1::G00021

Group size22 locus tags listed below.

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

Context span2480558-2484770Genomic interval covered by the local TCS group.

Identifiers

Old locus tagSFV_2429RefSeq proteinWP_005070035.1

Context group IDGCF_000013585::NC_008258.1::G00021

Context members

SFV_RS13515SFV_RS13520

Partner locus tags

SFV_RS13515SFV_RS13520

Partner old locus tags

SFV_2428SFV_2429

Partner protein IDs

WP_000991377.1 WP_005070035.1

External references

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

RefSeqWP_005070035.1Primary protein accession used for annex mappings.

UniProt accessionQ0T2C7Primary UniProt accession resolved in the annex database.

UniProt IDQ0T2C7_SHIF8Display 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

16822325

Genomic coordinates

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

Current locus tagSFV_RS13520Primary locus identifier stored in the genes table.

Old locus tagSFV_2429Legacy locus tag recovered from the local context mapping.

Contig / repliconNC_008258.1Sequence record reported by the local genomic context database.

Genomic interval2 481 177-2 484 770 nt3 594 nt · Forward (+)

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

Local TCS group span2 480 558-2 484 770 ntGCF_000013585::NC_008258.1::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_000013585::NC_008258.1::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_008258.1All displayed genes belong to this local TCS context.

Neighborhood span2 480 558-2 484 770 nt4 213 nt

Members21 current focus gene

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

2 480 558 nt2 484 770 nt

+-SFV_RS13515 SFV_RS13520

Neighborhood gene cards

2 genes in the current local neighborhood.

SFV_RS13515GCF_000013585#SFV_RS13515

RRunclassified

2 480 558-2 481 172 nt · Forward (+)

Old locus SFV_2428RefSeq WP_000991377.1

Open gene

SFV_RS13520GCF_000013585#SFV_RS13520

HKUnorthodoxCurrent focus

2 481 177-2 484 770 nt · Forward (+)

Old locus SFV_2429RefSeq WP_005070035.1

Open current gene

Clusters

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

Available memberships1 cluster

HKOC_0161015HK

Run 6102 sequencesid 100%cov 80%

PFAM SBP_bac_3 + SBP_bac_3 + HisKA + HATPase_c + Response_reg

Current gene is the representative sequence.

Selected clusterHKOC_0161015Run 6 · HK · 102 sequences

Representative sequenceGCF_000013585#SFV_RS13520The current gene is the representative for this cluster.

PFAM architectureSBP_bac_3 + SBP_bac_3 + HisKA + HATPase_c + Response_reg5 domains in the representative PFAM annotation.

Open in cluster search

PFAM architecture for HKOC_0161015

Simplified PFAM architecture for HKOC_0161015

PFAM domain coverage: 720 / 1197 aa (60.2%)

1 aa1197 aa

SBP_bac_3SBP_bac_3HisKAHATPase_cResponse_reg

Simplified architecture: SBP_bac_3 + SBP_bac_3 + HisKA + HATPase_c + Response_reg
Raw architecture: SBP_bac_3[62-276] | SBP_bac_3[306-520] | HisKA[711-777] | HATPase_c[825-937] | Response_reg[961-1070]
Domain count: 5
Matched identifier: HKOC_0161015
Positioned domains: SBP_bac_3 62-276 ; SBP_bac_3 306-520 ; HisKA 711-777 ; HATPase_c 825-937 ; Response_reg 961-1070

Cluster members and taxonomy

Representative gene: GCF_000013585#SFV_RS13520

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

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

Related genes

Preview from the same derived genome key