Gene detail

FNFX1_RS08770

Response regulator OmpR family

Francisella cf. novicida Fx1 · GCF_000195535

Open genome Open selected cluster RefSeq

ClassRRTypeOmpRLength228 aaTM0ValidatedNoCompleteYesContextpaired

Gene IDGCF_000195535#FNFX1_RS08770Stable P2CS identifier used across views.

GenomeGCF_000195535Bacteria; Pseudomonadati; Pseudomonadota; Gammaproteobacteria; Thiotrichales; Francisellaceae; Francisella

Selected clusterRROC_1302559Run 7 · 1 sequences · id 100% · cov 80% · representative

External referencesWP_014550310.1 · MIST4 FNFX1_RS08770RefSeq · MIST4

Domain signature

Compact overview inferred from the domain field

Response_regTrans_reg_C

Protein length228 aaLength used to scale native and Biotite-like views.

Annotated domains22 with usable coordinates.

Domain coverage186 / 228 aa (81.6%)Merged over positioned domains only.

Domain description1 Response_reg,1 Trans_reg_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

Domain view

Native Biotite-like

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

1 aa228 aa

Domain-by-domain annotation2 items

1 Response_reg#1

5-114 aa · 110 aa · 48.2% of protein

Raw tokenResponse_reg:5:8.93e-29:114:111:111

2 Trans_reg_C#2

149-224 aa · 76 aa · 33.3% of protein

Raw tokenTrans_reg_C:149:8.08e-22:224:77:77

Raw architecture: Response_reg:5:8.93e-29:114:111:111#Trans_reg_C:149:8.08e-22:224:77:77
Domain description: 1 Response_reg,1 Trans_reg_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_000195535::NC_017450.1::G00004

Group size22 locus tags listed below.

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

Context span1840955-1844364Genomic interval covered by the local TCS group.

Identifiers

Old locus tagFNFX1_1755RefSeq proteinWP_014550310.1

Context group IDGCF_000195535::NC_017450.1::G00004

Context members

FNFX1_RS08770FNFX1_RS08775

Partner locus tags

FNFX1_RS08770FNFX1_RS08775

Partner old locus tags

FNFX1_1755FNFX1_1756

Partner protein IDs

WP_014550310.1 WP_014550311.1

External references

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

No UniProt / GO / PubMed mapping was found for WP_014550310.1.

Genomic coordinates

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

Current locus tagFNFX1_RS08770Primary locus identifier stored in the genes table.

Old locus tagFNFX1_1755Legacy locus tag recovered from the local context mapping.

Contig / repliconNC_017450.1Sequence record reported by the local genomic context database.

Genomic interval1 840 955-1 841 641 nt687 nt · Reverse (-)

StrandReverse (-)Strand sign follows the local context database convention.

Local TCS group span1 840 955-1 844 364 ntGCF_000195535::NC_017450.1::G00004

Quick actions

Open genome Search genes in genome

Local neighborhood

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

GCF_000195535::NC_017450.1::G00004

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_017450.1All displayed genes belong to this local TCS context.

Neighborhood span1 840 955-1 844 364 nt3 410 nt

Members21 current focus gene

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

1 840 955 nt1 844 364 nt

+-FNFX1_RS08770 FNFX1_RS08775

Neighborhood gene cards

2 genes in the current local neighborhood.

FNFX1_RS08770GCF_000195535#FNFX1_RS08770

RROmpRCurrent focus

1 840 955-1 841 641 nt · Reverse (-)

Old locus FNFX1_1755RefSeq WP_014550310.1

Open current gene

FNFX1_RS08775GCF_000195535#FNFX1_RS08775

HKClassic

1 841 683-1 844 364 nt · Reverse (-)

Old locus FNFX1_1756RefSeq WP_014550311.1

Open gene

Clusters

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

Available memberships1 cluster

RROC_1302559RR

Run 71 sequencesid 100%cov 80%

PFAM Response_reg + Trans_reg_C

Current gene is the representative sequence.

Selected clusterRROC_1302559Run 7 · RR · 1 sequences

Representative sequenceGCF_000195535#FNFX1_RS08770The current gene is the representative for this cluster.

PFAM architectureResponse_reg + Trans_reg_C2 domains in the representative PFAM annotation.

Open in cluster search

PFAM architecture for RROC_1302559

Simplified PFAM architecture for RROC_1302559

PFAM domain coverage: 185 / 228 aa (81.1%)

1 aa228 aa

Response_regTrans_reg_C

Simplified architecture: Response_reg + Trans_reg_C
Raw architecture: Response_reg[5-114] | Trans_reg_C[150-224]
Domain count: 2
Matched identifier: RROC_1302559
Positioned domains: Response_reg 5-114 ; Response_reg 5-114 ; Trans_reg_C 150-224 ; Trans_reg_C 150-224

Cluster members and taxonomy

Representative gene: GCF_000195535#FNFX1_RS08770

Sankey plot built from the taxonomy of all members in the selected cluster.

Genome taxonomy

Unknown

Taxonomy recordUnknownTaxon ID 984 129 · GCF_000195535

AssemblyASM19553v1 · Complete Genomehaploid

Genome composition1 913 619 bp · 32,5% GCFrancisella cf. novicida Fx1

Signal transduction countsGenes 6 · HK 3 · RR 3CheA 0 · PP 0

Ranked taxonomy7 ranked levels available

SuperkingdomBacteriaKingdomPseudomonadatiPhylumPseudomonadotaClassGammaproteobacteriaOrderThiotrichalesFamilyFrancisellaceaeGenusFrancisella

Lineage path7 lineage nodes

1Bacteria2Pseudomonadati3Pseudomonadota4Gammaproteobacteria5Thiotrichales6Francisellaceae7Francisella

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

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Preview from the same derived genome key