Gene detail

Detailed information of g256.t1 in Calvadosia cruxmelitensis

Genomic Location: not available for this species
NR annotation: OGG94869.1, flagellar biosynthesis protein FlhF [Candidatus Lambdaproteobacteria bacterium RIFOXYD2_FULL_50_16]
Species Calvadosia cruxmelitensis · all data for this species · gene families

Sequence

Sequence data are not available for Calvadosia cruxmelitensis.
Nucleotide and protein sequences are provided for the species whose genome annotation is complete (see annotated genomes); for this species only the assembly is archived. The functional annotation below is likewise unavailable.

UniProt (Swiss-Prot top hit)

UniProt accession	Description
Q01960	Flagellar biosynthesis protein FlhF OS=Bacillus subtilis (strain 168) OX=224308 GN=flhF PE=1 SV=1
O52908	Flagellar biosynthesis protein FlhF OS=Campylobacter jejuni subsp. jejuni serotype O:2 (strain ATCC 700819 / NCTC 11168) OX=192222 GN=flhF PE=3 SV=2
Q9ZM34	Flagellar biosynthesis protein FlhF OS=Helicobacter pylori (strain J99 / ATCC 700824) OX=85963 GN=flhF PE=3 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0000001 (this species only) · gene tree & orthology
Orthogroup (gene family)	OG0000009 (this species only) · gene tree & orthology
Orthogroup (gene family)	OG0000060 (this species only) · gene tree & orthology
Orthogroup (gene family)	OG0001054 (this species only) · gene tree & orthology
Orthogroup (gene family)	OG0003169 (this species only) · gene tree & orthology
Orthogroup (gene family)	OG0005738 (this species only) · gene tree & orthology
Orthogroup (gene family)	OG0007709 (this species only) · gene tree & orthology
Orthogroup (gene family)	OG0012246 (this species only) · gene tree & orthology
Orthogroup (gene family)	OG0022449 (this species only) · gene tree & orthology
Orthogroup (gene family)	OG0023496 (this species only) · gene tree & orthology
Orthogroup (gene family)	OG0049858 (this species only) · gene tree & orthology
Ubiquitin family	UBD\|Other\|Beta-prp · all ubiquitin genes in this species
Ubiquitin family	E3\|E3 adaptor Cullin RING\|CDC20 · all ubiquitin genes in this species
Ubiquitin family	E3\|E3 adaptor Cullin RING\|DWD · all ubiquitin genes in this species

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF00665 all species →	rve	Integrase core domain	Domain	Interproscan
PF00415 all species →	RCC1	Regulator of chromosome condensation (RCC1) repeat	Repeat	Interproscan
PF00400 all species →	WD40	WD domain, G-beta repeat	Repeat	Interproscan
PF00448 all species →	SRP54	SRP54-type protein, GTPase domain	Domain	Interproscan
PF13359 all species →	DDE_Tnp_4	DDE superfamily endonuclease	Domain	Interproscan
PF00006 all species →	ATP-synt_ab	ATP synthase alpha/beta family, nucleotide-binding domain	Domain	Interproscan
PF07497 all species →	Rho_RNA_bind	Rho termination factor, RNA-binding domain	Domain	Interproscan
PF07498 all species →	Rho_N	Rho termination factor, N-terminal domain	Domain	Interproscan
PF00095 all species →	WAP	WAP-type (Whey Acidic Protein) 'four-disulfide core'	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR007122 all species →	Family	Villin/Gelsolin	Interproscan
IPR029006 all species →	Homologous_superfamily	ADF-H/Gelsolin-like domain superfamily	Interproscan
IPR036397 all species →	Homologous_superfamily	Ribonuclease H superfamily	Interproscan
IPR012337 all species →	Homologous_superfamily	Ribonuclease H-like superfamily	Interproscan
IPR001584 all species →	Domain	Integrase, catalytic core	Interproscan
IPR050951 all species →	Family	Retrovirus-related Pol polyprotein	Interproscan
IPR043502 all species →	Homologous_superfamily	DNA/RNA polymerase superfamily	Interproscan
IPR043128 all species →	Homologous_superfamily	Reverse transcriptase/Diguanylate cyclase domain	Interproscan
IPR000408 all species →	Repeat	Regulator of chromosome condensation, RCC1	Interproscan
IPR051553 all species →	Family	Ran GTPase-activating	Interproscan
IPR009091 all species →	Homologous_superfamily	Regulator of chromosome condensation 1/beta-lactamase-inhibitor protein II	Interproscan
IPR015943 all species →	Homologous_superfamily	WD40/YVTN repeat-like-containing domain superfamily	Interproscan
IPR001680 all species →	Repeat	WD40 repeat	Interproscan
IPR027145 all species →	Family	Periodic tryptophan protein 2	Interproscan
IPR020472 all species →	Repeat	G-protein beta WD-40 repeat	Interproscan
IPR019775 all species →	Conserved_site	WD40 repeat, conserved site	Interproscan
IPR036322 all species →	Homologous_superfamily	WD40-repeat-containing domain superfamily	Interproscan
IPR047040 all species →	Domain	Flagellar biosynthesis protein FlhF, GTPase domain	Interproscan
IPR000897 all species →	Domain	Signal recognition particle, SRP54 subunit, GTPase domain	Interproscan
IPR027417 all species →	Homologous_superfamily	P-loop containing nucleoside triphosphate hydrolase	Interproscan
IPR003593 all species →	Domain	AAA+ ATPase domain	Interproscan
IPR020006 all species →	Family	Flagellar biosynthesis protein FlhF	Interproscan
IPR027806 all species →	Domain	Harbinger transposase-derived nuclease domain	Interproscan
IPR011113 all species →	Domain	Rho termination factor, RNA-binding domain	Interproscan
IPR041703 all species →	Domain	Transcription termination factor Rho, ATP binding domain	Interproscan
IPR011112 all species →	Domain	Rho termination factor, N-terminal	Interproscan
IPR004665 all species →	Family	Transcription termination factor Rho	Interproscan
IPR000194 all species →	Domain	ATPase, F1/V1/A1 complex, alpha/beta subunit, nucleotide-binding domain	Interproscan
IPR012340 all species →	Homologous_superfamily	Nucleic acid-binding, OB-fold	Interproscan
IPR036269 all species →	Homologous_superfamily	Rho termination factor, N-terminal domain superfamily	Interproscan
IPR011129 all species →	Domain	Cold shock domain	Interproscan
IPR008197 all species →	Domain	WAP-type 'four-disulfide core' domain	Interproscan
IPR036645 all species →	Homologous_superfamily	Elafin-like superfamily	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR11977 all species →	VILLIN	Interproscan
PTHR37984 all species →	PROTEIN CBG26694	Interproscan
PTHR45982 all species →	REGULATOR OF CHROMOSOME CONDENSATION	Interproscan
PTHR19858 all species →	WD40 REPEAT PROTEIN	Interproscan
PTHR43134 all species →	SIGNAL RECOGNITION PARTICLE RECEPTOR SUBUNIT ALPHA	Interproscan
PTHR23080 all species →	THAP DOMAIN PROTEIN	Interproscan
PTHR46425 all species →	TRANSCRIPTION TERMINATION FACTOR RHO	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0051015 all species →	Molecular Function	actin filament binding	Interproscan
GO:0005546 all species →	Molecular Function	phosphatidylinositol-4,5-bisphosphate binding	Interproscan
GO:0005737 all species →	Cellular Component	cytoplasm	Interproscan
GO:0008154 all species →	Biological Process	actin polymerization or depolymerization	Interproscan
GO:0015629 all species →	Cellular Component	actin cytoskeleton	Interproscan
GO:0051014 all species →	Biological Process	actin filament severing	Interproscan
GO:0051016 all species →	Biological Process	barbed-end actin filament capping	Interproscan
GO:0003676 all species →	Molecular Function	nucleic acid binding	Interproscan
GO:0015074 all species →	Biological Process	DNA integration	Interproscan
GO:0005085 all species →	Molecular Function	guanyl-nucleotide exchange factor activity	Interproscan
GO:0005515 all species →	Molecular Function	protein binding	Interproscan
GO:0000028 all species →	Biological Process	ribosomal small subunit assembly	Interproscan
GO:0000462 all species →	Biological Process	maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)	Interproscan
GO:0032040 all species →	Cellular Component	small-subunit processome	Interproscan
GO:0034388 all species →	Cellular Component	Pwp2p-containing subcomplex of 90S preribosome	Interproscan
GO:0003924 all species →	Molecular Function	GTPase activity	Interproscan
GO:0005525 all species →	Molecular Function	GTP binding	Interproscan
GO:0006614 all species →	Biological Process	SRP-dependent cotranslational protein targeting to membrane	Interproscan
GO:0005047 all species →	Molecular Function	signal recognition particle binding	Interproscan
GO:0005886 all species →	Cellular Component	plasma membrane	Interproscan
GO:0006605 all species →	Biological Process	protein targeting	Interproscan
GO:0016020 all species →	Cellular Component	membrane	Interproscan
GO:0016887 all species →	Molecular Function	ATP hydrolysis activity	Interproscan
GO:0044781 all species →	Biological Process	bacterial-type flagellum organization	Interproscan
GO:0003723 all species →	Molecular Function	RNA binding	Interproscan
GO:0006353 all species →	Biological Process	DNA-templated transcription termination	Interproscan
GO:0005524 all species →	Molecular Function	ATP binding	Interproscan
GO:0008186 all species →	Molecular Function	ATP-dependent activity, acting on RNA	Interproscan
GO:0005576 all species →	Cellular Component	extracellular region	Interproscan
GO:0030414 all species →	Molecular Function	peptidase inhibitor activity	Interproscan

Search by domain instead of by gene. Any accession above (InterPro, Pfam, PANTHER, GO, KEGG) can be used as a query on the Functional Domain Search page, which searches all 148 annotated genomes at once.

KEGG pathway

KO	Enzyme	Enzyme ID	Pathway	Map ID	Source
K02404	flhF; flagellar biosynthesis protein FlhF	-	Bacterial motility proteins	ko02035	deepkoala
K03628	rho; transcription termination factor Rho	-	Messenger RNA biogenesis	ko03019	deepkoala
K14830	MAK11, PAK1IP1; protein MAK11	-	Ribosome biogenesis	ko03009	deepkoala

Searching by KO or pathway ID across all species is available on the KEGG Pathway page.

Co-expression network

Genes whose expression across the transcriptome samples of Calvadosia cruxmelitensis tracks this one. Counts are over the whole network; the network view itself draws at most 100 partners per query gene (CNIDO_NET_TOP_K), so a hub gene can show fewer edges than the number below.

No co-expression network has been built for this species, so this gene has no partners to show. Networks are available for the species listed on the Network Analysis page.

Single-cell expression

Whether this gene can be visualised in the single-cell atlases of Calvadosia cruxmelitensis, and in which cell types it is a marker. Expression is stored per cell, so the violin plot and the cell-type means are computed in the viewer — open a dataset to see them.

No single-cell dataset has been published for this species. The atlases that do exist are listed in the Cell Atlas.

Epigenetic marks

Chromatin and DNA-methylation data covering this gene. Peak calls are listed per sample with the genomic region the peak falls in; DNA methylation is listed as sample availability only, because those tables are queried by the DNA Methylation page itself.

No epigenomic data has been deposited for this species. The assays that exist across the site are described in the Epigenomic Data module.

What you can do with this gene

Every tool below opens with this gene already entered, so you land on the analysis rather than on an empty form. Links open in a new tab.

Analysis	What it does	Status
Primer design	Design PCR / qPCR primers on this gene’s sequence with the published primer3 settings. Opens with the primers already computed.	sequence table not available	–
BLAST	Search this gene’s sequence against the CnidoSite BLAST databases. The query is filled in and the species’ database is preselected — press Run to start.	sequence table not available	–
Expression heatmap	Draw this gene’s expression as a heatmap across all RNA-seq samples, and compare it with the genes you add next to it.	no expression matrix	–
Gene family / orthogroup	Look this gene up in the single-copy orthogroups built from the high-quality cnidarian genomes, and see which other species carry an orthologue.		open →
Gene set analysis	Start a gene-set enrichment analysis with this gene as the seed list. Add more genes on that page before running it.		open →