Gene detail

Detailed information of g541.t1 in Calvadosia cruxmelitensis

Genomic Location: not available for this species
NR annotation: MCG6890205.1, outer membrane protein transport protein [Gammaproteobacteria 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
F1QCV2	Polyamine deacetylase HDAC10 OS=Danio rerio OX=7955 GN=hdac10 PE=1 SV=2
Q9Z2V5	Protein deacetylase HDAC6 OS=Mus musculus OX=10090 GN=Hdac6 PE=1 SV=3
Q9UBN7	Protein deacetylase HDAC6 OS=Homo sapiens OX=9606 GN=HDAC6 PE=1 SV=2

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0000001 (this species only) · gene tree & orthology
Orthogroup (gene family)	OG0000300 (this species only) · gene tree & orthology
Orthogroup (gene family)	OG0000990 (this species only) · gene tree & orthology
Orthogroup (gene family)	OG0001107 (this species only) · gene tree & orthology
Orthogroup (gene family)	OG0003557 (this species only) · gene tree & orthology
Orthogroup (gene family)	OG0005588 (this species only) · gene tree & orthology
Orthogroup (gene family)	OG0005774 (this species only) · gene tree & orthology
Orthogroup (gene family)	OG0006386 (this species only) · gene tree & orthology
Orthogroup (gene family)	OG0013356 (this species only) · gene tree & orthology
Orthogroup (gene family)	OG0014540 (this species only) · gene tree & orthology
Orthogroup (gene family)	OG0033344 (this species only) · gene tree & orthology
Orthogroup (gene family)	OG0037198 (this species only) · gene tree & orthology
Orthogroup (gene family)	OG0060656 (this species only) · gene tree & orthology
Orthogroup (gene family)	OG0061966 (this species only) · gene tree & orthology
Ubiquitin family	E3\|E3 activity\|HECT · all ubiquitin genes in this species

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF03349 all species →	Toluene_X	Outer membrane protein transport protein (OMPP1/FadL/TodX)	Family	Interproscan
PF01618 all species →	MotA_ExbB	MotA/TolQ/ExbB proton channel family	Family	Interproscan
PF13193 all species →	AMP-binding_C	AMP-binding enzyme C-terminal domain	Domain	Interproscan
PF00501 all species →	AMP-binding	AMP-binding enzyme	Family	Interproscan
PF00632 all species →	HECT	HECT-domain (ubiquitin-transferase)	Domain	Interproscan
PF00264 all species →	Tyrosinase	Common central domain of tyrosinase	Domain	Interproscan
PF13880 all species →	Acetyltransf_13	ESCO1/2 acetyl-transferase	Domain	Interproscan
PF00850 all species →	Hist_deacetyl	Histone deacetylase domain	Domain	Interproscan
PF03372 all species →	Exo_endo_phos	Endonuclease/Exonuclease/phosphatase family	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR005017 all species →	Family	Outer membrane protein transport protein (OMPP1/FadL/TodX)	Interproscan
IPR012337 all species →	Homologous_superfamily	Ribonuclease H-like superfamily	Interproscan
IPR036691 all species →	Homologous_superfamily	Endonuclease/exonuclease/phosphatase superfamily	Interproscan
IPR000540 all species →	Conserved_site	Flagellar motor protein MotA, conserved site	Interproscan
IPR002898 all species →	Domain	MotA/TolQ/ExbB proton channel	Interproscan
IPR047055 all species →	Family	Motility protein A-like	Interproscan
IPR001478 all species →	Domain	PDZ domain	Interproscan
IPR036034 all species →	Homologous_superfamily	PDZ superfamily	Interproscan
IPR025110 all species →	Domain	AMP-binding enzyme, C-terminal domain	Interproscan
IPR042099 all species →	Homologous_superfamily	ANL, N-terminal domain	Interproscan
IPR020845 all species →	Conserved_site	AMP-binding, conserved site	Interproscan
IPR045851 all species →	Homologous_superfamily	AMP-binding enzyme, C-terminal domain superfamily	Interproscan
IPR000873 all species →	Domain	AMP-dependent synthetase/ligase domain	Interproscan
IPR000569 all species →	Domain	HECT domain	Interproscan
IPR035983 all species →	Homologous_superfamily	HECT, E3 ligase catalytic domain	Interproscan
IPR021109 all species →	Homologous_superfamily	Aspartic peptidase domain superfamily	Interproscan
IPR008922 all species →	Homologous_superfamily	Di-copper centre-containing domain superfamily	Interproscan
IPR002227 all species →	Domain	Tyrosinase copper-binding domain	Interproscan
IPR028009 all species →	Domain	N-acetyltransferase ESCO, acetyl-transferase domain	Interproscan
IPR000286 all species →	Family	Histone deacetylase family	Interproscan
IPR023696 all species →	Homologous_superfamily	Ureohydrolase domain superfamily	Interproscan
IPR023801 all species →	Domain	Histone deacetylase domain	Interproscan
IPR050284 all species →	Family	Histone deacetylase and polyamine deacetylase	Interproscan
IPR037138 all species →	Homologous_superfamily	Histone deacetylase domain superfamily	Interproscan
IPR005135 all species →	Domain	Endonuclease/exonuclease/phosphatase	Interproscan
IPR050410 all species →	Family	CCR4/nocturin mRNA turnover and transcription	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR35093 all species →	OUTER MEMBRANE PROTEIN NMB0088-RELATED	Interproscan
PTHR30433 all species →	CHEMOTAXIS PROTEIN MOTA	Interproscan
PTHR43347 all species →	ACYL-COA SYNTHETASE	Interproscan
PTHR45884 all species →	N-ACETYLTRANSFERASE ECO	Interproscan
PTHR10625 all species →	HISTONE DEACETYLASE HDAC1-RELATED	Interproscan
PTHR12121 all species →	CARBON CATABOLITE REPRESSOR PROTEIN 4	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0015483 all species →	Molecular Function	long-chain fatty acid transporting porin activity	Interproscan
GO:0005886 all species →	Cellular Component	plasma membrane	Interproscan
GO:0006935 all species →	Biological Process	chemotaxis	Interproscan
GO:0016021 all species →	Cellular Component	membrane	Interproscan
GO:0071978 all species →	Biological Process	bacterial-type flagellum-dependent swarming motility	Interproscan
GO:0005515 all species →	Molecular Function	protein binding	Interproscan
GO:0005759 all species →	Cellular Component	mitochondrial matrix	Interproscan
GO:0050218 all species →	Molecular Function	propionate-CoA ligase activity	Interproscan
GO:0004842 all species →	Molecular Function	ubiquitin-protein transferase activity	Interproscan
GO:0016491 all species →	Molecular Function	oxidoreductase activity	Interproscan
GO:0000785 all species →	Cellular Component	chromatin	Interproscan
GO:0005634 all species →	Cellular Component	nucleus	Interproscan
GO:0007064 all species →	Biological Process	mitotic sister chromatid cohesion	Interproscan
GO:0061733 all species →	Molecular Function	peptide-lysine-N-acetyltransferase activity	Interproscan
GO:0000118 all species →	Cellular Component	histone deacetylase complex	Interproscan
GO:0000122 all species →	Biological Process	negative regulation of transcription by RNA polymerase II	Interproscan
GO:0004407 all species →	Molecular Function	histone deacetylase activity	Interproscan
GO:0008134 all species →	Molecular Function	transcription factor binding	Interproscan
GO:0016575 all species →	Biological Process	obsolete histone deacetylation	Interproscan
GO:0003824 all species →	Molecular Function	catalytic activity	Interproscan
GO:0000175 all species →	Molecular Function	3'-5'-RNA exonuclease 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
K01908	ACSS3, prpE; propionyl-CoA synthetase	EC:6.2.1.17	Lipid biosynthesis proteins	ko01004	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 →