Gene detail

Detailed information of g67.t1 in Calvadosia cruxmelitensis

Genomic Location: not available for this species
NR annotation: PCI27347.1, flagellar motor switch protein FliM [SAR324 cluster bacterium]
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
Q51465	Flagellar motor switch protein FliM OS=Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1) OX=208964 GN=fliM PE=3 SV=2
P26418	Flagellar motor switch protein FliM OS=Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720) OX=99287 GN=fliM PE=1 SV=1
P06974	Flagellar motor switch protein FliM OS=Escherichia coli (strain K12) OX=83333 GN=fliM PE=1 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0000006 (this species only) · gene tree & orthology
Orthogroup (gene family)	OG0000220 (this species only) · gene tree & orthology
Orthogroup (gene family)	OG0000437 (this species only) · gene tree & orthology
Orthogroup (gene family)	OG0000463 (this species only) · gene tree & orthology
Orthogroup (gene family)	OG0002880 (this species only) · gene tree & orthology
Orthogroup (gene family)	OG0003131 (this species only) · gene tree & orthology
Orthogroup (gene family)	OG0003694 (this species only) · gene tree & orthology
Orthogroup (gene family)	OG0007917 (this species only) · gene tree & orthology
Orthogroup (gene family)	OG0013022 (this species only) · gene tree & orthology
Orthogroup (gene family)	OG0015209 (this species only) · gene tree & orthology
Orthogroup (gene family)	OG0033272 (this species only) · gene tree & orthology
Orthogroup (gene family)	OG0061804 (this species only) · gene tree & orthology
Orthogroup (gene family)	OG0061844 (this species only) · gene tree & orthology

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF10442 all species →	FIST_C	FIST C domain	Domain	Interproscan
PF02154 all species →	FliM	Flagellar motor switch protein FliM	Family	Interproscan
PF01052 all species →	FliMN_C	Type III flagellar switch regulator (C-ring) FliN C-term	Family	Interproscan
PF00076 all species →	RRM_1	RNA recognition motif	Domain	Interproscan
PF00078 all species →	RVT_1	Reverse transcriptase (RNA-dependent DNA polymerase)	Domain	Interproscan
PF00557 all species →	Peptidase_M24	Metallopeptidase family M24	Domain	Interproscan
PF05195 all species →	AMP_N	Aminopeptidase P, N-terminal domain	Domain	Interproscan
PF00106 all species →	adh_short	short chain dehydrogenase	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR019494 all species →	Domain	FIST, C-domain	Interproscan
IPR015943 all species →	Homologous_superfamily	WD40/YVTN repeat-like-containing domain superfamily	Interproscan
IPR036322 all species →	Homologous_superfamily	WD40-repeat-containing domain superfamily	Interproscan
IPR052035 all species →	Family	Zinc finger BED domain-containing	Interproscan
IPR012337 all species →	Homologous_superfamily	Ribonuclease H-like superfamily	Interproscan
IPR001689 all species →	Family	Flagellar motor switch protein FliM	Interproscan
IPR028976 all species →	Homologous_superfamily	CheC-like superfamily	Interproscan
IPR036429 all species →	Homologous_superfamily	SpoA-like superfamily	Interproscan
IPR001543 all species →	Domain	Flagellar motor switch protein FliN-like, C-terminal domain	Interproscan
IPR000504 all species →	Domain	RNA recognition motif domain	Interproscan
IPR012677 all species →	Homologous_superfamily	Nucleotide-binding alpha-beta plait domain superfamily	Interproscan
IPR035979 all species →	Homologous_superfamily	RNA-binding domain superfamily	Interproscan
IPR006529 all species →	Family	U2 snRNP auxilliary factor, large subunit, splicing factor	Interproscan
IPR000477 all species →	Domain	Reverse transcriptase domain	Interproscan
IPR043502 all species →	Homologous_superfamily	DNA/RNA polymerase superfamily	Interproscan
IPR043128 all species →	Homologous_superfamily	Reverse transcriptase/Diguanylate cyclase domain	Interproscan
IPR036005 all species →	Homologous_superfamily	Creatinase/aminopeptidase-like	Interproscan
IPR000994 all species →	Domain	Peptidase M24	Interproscan
IPR007865 all species →	Domain	Aminopeptidase P, N-terminal	Interproscan
IPR029149 all species →	Homologous_superfamily	Creatinase/Aminopeptidase P/Spt16, N-terminal	Interproscan
IPR009060 all species →	Homologous_superfamily	UBA-like superfamily	Interproscan
IPR003892 all species →	Domain	Ubiquitin system component CUE	Interproscan
IPR002347 all species →	Family	Short-chain dehydrogenase/reductase SDR	Interproscan
IPR020904 all species →	Conserved_site	Short-chain dehydrogenase/reductase, conserved site	Interproscan
IPR036291 all species →	Homologous_superfamily	NAD(P)-binding domain superfamily	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR14939 all species →	F-BOX ONLY PROTEIN 22	Interproscan
PTHR46481 all species →	ZINC FINGER BED DOMAIN-CONTAINING PROTEIN 4	Interproscan
PTHR30034 all species →	FLAGELLAR MOTOR SWITCH PROTEIN FLIM	Interproscan
PTHR23139 all species →	RNA-BINDING PROTEIN	Interproscan
PTHR19446 all species →	REVERSE TRANSCRIPTASES	Interproscan
PTHR43226 all species →	XAA-PRO AMINOPEPTIDASE 3	Interproscan
PTHR12493 all species →	CUE DOMAIN CONTAINING 2	Interproscan
PTHR43313 all species →	SHORT-CHAIN DEHYDROGENASE/REDUCTASE FAMILY 9C	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0000209 all species →	Biological Process	protein polyubiquitination	Interproscan
GO:0032436 all species →	Biological Process	positive regulation of proteasomal ubiquitin-dependent protein catabolic process	Interproscan
GO:0005515 all species →	Molecular Function	protein binding	Interproscan
GO:0003774 all species →	Molecular Function	cytoskeletal motor activity	Interproscan
GO:0009425 all species →	Cellular Component	bacterial-type flagellum basal body	Interproscan
GO:0071973 all species →	Biological Process	bacterial-type flagellum-dependent cell motility	Interproscan
GO:0050918 all species →	Biological Process	positive chemotaxis	Interproscan
GO:0071978 all species →	Biological Process	bacterial-type flagellum-dependent swarming motility	Interproscan
GO:0003723 all species →	Molecular Function	RNA binding	Interproscan
GO:0000243 all species →	Cellular Component	commitment complex	Interproscan
GO:0008187 all species →	Molecular Function	poly-pyrimidine tract binding	Interproscan
GO:0016607 all species →	Cellular Component	nuclear speck	Interproscan
GO:0030628 all species →	Molecular Function	pre-mRNA 3'-splice site binding	Interproscan
GO:0071004 all species →	Cellular Component	U2-type prespliceosome	Interproscan
GO:0089701 all species →	Cellular Component	U2AF complex	Interproscan
GO:0003676 all species →	Molecular Function	nucleic acid binding	Interproscan
GO:0005634 all species →	Cellular Component	nucleus	Interproscan
GO:0006397 all species →	Biological Process	mRNA processing	Interproscan
GO:0030145 all species →	Molecular Function	manganese ion binding	Interproscan
GO:0070006 all species →	Molecular Function	metalloaminopeptidase activity	Interproscan
GO:0004177 all species →	Molecular Function	aminopeptidase activity	Interproscan
GO:0005739 all species →	Cellular Component	mitochondrion	Interproscan
GO:0006508 all species →	Biological Process	proteolysis	Interproscan
GO:0008233 all species →	Molecular Function	peptidase activity	Interproscan
GO:0043130 all species →	Molecular Function	ubiquitin binding	Interproscan
GO:0016491 all species →	Molecular Function	oxidoreductase activity	Interproscan
GO:0008202 all species →	Biological Process	steroid metabolic process	Interproscan
GO:0043231 all species →	Cellular Component	intracellular membrane-bounded organelle	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
K01262	pepP; Xaa-Pro aminopeptidase	EC:3.4.11.9	Peptidases and inhibitors	ko01002	deepkoala
K02416	fliM; flagellar motor switch protein FliM	-	Bacterial motility proteins	ko02035	deepkoala
K12837	U2AF2; splicing factor U2AF 65 kDa subunit	-	Spliceosome	ko03041	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 →