Gene detail

Detailed information of g372.t1 in Calvadosia cruxmelitensis

Genomic Location: not available for this species
NR annotation: WP_207570214.1, restriction endonuclease subunit S [Shewanella sp. 4t3-1-2LB]
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
P10485	Type I restriction enzyme EcoR124I/EcoR124II specificity subunit OS=Escherichia coli OX=562 GN=hsdS PE=1 SV=2
P17222	Type I restriction enzyme EcoprrI specificity subunit OS=Escherichia coli OX=562 GN=prrB PE=3 SV=1
P71344	Putative type I restriction enzyme specificity subunit S.HindORF215P OS=Haemophilus influenzae (strain ATCC 51907 / DSM 11121 / KW20 / Rd) OX=71421 GN=HI_0216 PE=3 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0000109 (this species only) · gene tree & orthology
Orthogroup (gene family)	OG0000757 (this species only) · gene tree & orthology
Orthogroup (gene family)	OG0001094 (this species only) · gene tree & orthology
Orthogroup (gene family)	OG0004672 (this species only) · gene tree & orthology
Orthogroup (gene family)	OG0005219 (this species only) · gene tree & orthology
Orthogroup (gene family)	OG0005732 (this species only) · gene tree & orthology
Orthogroup (gene family)	OG0015599 (this species only) · gene tree & orthology
Orthogroup (gene family)	OG0026265 (this species only) · gene tree & orthology
Orthogroup (gene family)	OG0035701 (this species only) · gene tree & orthology
Orthogroup (gene family)	OG0061618 (this species only) · gene tree & orthology

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF13183 all species →	Fer4_8	4Fe-4S dicluster domain	Domain	Interproscan
PF01565 all species →	FAD_binding_4	FAD binding domain	Domain	Interproscan
PF02913 all species →	FAD-oxidase_C	FAD linked oxidases, C-terminal domain	Domain	Interproscan
PF01420 all species →	Methylase_S	Type I restriction modification DNA specificity domain	Domain	Interproscan
PF00106 all species →	adh_short	short chain dehydrogenase	Domain	Interproscan
PF01568 all species →	Molydop_binding	Molydopterin dinucleotide binding domain	Domain	Interproscan
PF02108 all species →	FliH	Flagellar assembly protein FliH	Family	Interproscan
PF00093 all species →	VWC	von Willebrand factor type C domain	Domain	Interproscan
PF00014 all species →	Kunitz_BPTI	Kunitz/Bovine pancreatic trypsin inhibitor domain	Domain	Interproscan
PF05375 all species →	Pacifastin_I	Pacifastin inhibitor (LCMII)	Family	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR016164 all species →	Homologous_superfamily	FAD-linked oxidase-like, C-terminal	Interproscan
IPR016171 all species →	Homologous_superfamily	Vanillyl-alcohol oxidase, C-terminal subdomain 2	Interproscan
IPR017896 all species →	Domain	4Fe-4S ferredoxin-type, iron-sulphur binding domain	Interproscan
IPR016166 all species →	Domain	FAD-binding domain, PCMH-type	Interproscan
IPR017900 all species →	Conserved_site	4Fe-4S ferredoxin, iron-sulphur binding, conserved site	Interproscan
IPR006094 all species →	Domain	FAD linked oxidase, N-terminal	Interproscan
IPR036318 all species →	Homologous_superfamily	FAD-binding, type PCMH-like superfamily	Interproscan
IPR004113 all species →	Domain	FAD-binding oxidoreductase/transferase, type 4, C-terminal	Interproscan
IPR016169 all species →	Homologous_superfamily	FAD-binding, type PCMH, subdomain 2	Interproscan
IPR039756 all species →	Family	Type II phosphatidylinositol 4-kinase Lsb6/PI4K2	Interproscan
IPR051212 all species →	Family	Type I restriction enzyme S subunit	Interproscan
IPR000055 all species →	Domain	Type I restriction modification DNA specificity domain	Interproscan
IPR044946 all species →	Homologous_superfamily	Type I restriction modification DNA specificity domain superfamily	Interproscan
IPR010031 all species →	Family	L-gulonolactone/D-arabinono-1,4-lactone oxidase-like	Interproscan
IPR036291 all species →	Homologous_superfamily	NAD(P)-binding domain superfamily	Interproscan
IPR020904 all species →	Conserved_site	Short-chain dehydrogenase/reductase, conserved site	Interproscan
IPR051721 all species →	Family	Biopterin synthesis and organic compound reduction	Interproscan
IPR002347 all species →	Family	Short-chain dehydrogenase/reductase SDR	Interproscan
IPR009010 all species →	Homologous_superfamily	Aspartate decarboxylase-like domain superfamily	Interproscan
IPR006657 all species →	Domain	Molybdopterin dinucleotide-binding domain	Interproscan
IPR018035 all species →	Domain	Flagellar assembly protein FliH/Type III secretion system HrpE	Interproscan
IPR052624 all species →	Family	Cysteine-rich motor neuron 1	Interproscan
IPR002223 all species →	Domain	Pancreatic trypsin inhibitor Kunitz domain	Interproscan
IPR036880 all species →	Homologous_superfamily	Pancreatic trypsin inhibitor Kunitz domain superfamily	Interproscan
IPR020901 all species →	Conserved_site	Proteinase inhibitor I2, Kunitz, conserved site	Interproscan
IPR001007 all species →	Domain	VWFC domain	Interproscan
IPR036201 all species →	Homologous_superfamily	Pacifastin domain superfamily	Interproscan
IPR008037 all species →	Domain	Pacifastin domain	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR11748 all species →	D-LACTATE DEHYDROGENASE	Interproscan
PTHR12865 all species →	PHOSPHATIDYLINOSITOL 4-KINASE TYPE-II	Interproscan
PTHR43140 all species →	TYPE-1 RESTRICTION ENZYME ECOKI SPECIFICITY PROTEIN	Interproscan
PTHR43762 all species →	L-GULONOLACTONE OXIDASE	Interproscan
PTHR44085 all species →	SEPIAPTERIN REDUCTASE	Interproscan
PTHR46704 all species →	CXC DOMAIN-CONTAINING PROTEIN-RELATED	Interproscan
PTHR43598 all species →	TUNGSTEN-CONTAINING FORMYLMETHANOFURAN DEHYDROGENASE 2 SUBUNIT B	Interproscan
PTHR46439 all species →	CYSTEINE-RICH MOTOR NEURON 1 PROTEIN	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0003824 all species →	Molecular Function	catalytic activity	Interproscan
GO:0050660 all species →	Molecular Function	flavin adenine dinucleotide binding	Interproscan
GO:0071949 all species →	Molecular Function	FAD binding	Interproscan
GO:0004430 all species →	Molecular Function	1-phosphatidylinositol 4-kinase activity	Interproscan
GO:0005765 all species →	Cellular Component	lysosomal membrane	Interproscan
GO:0005768 all species →	Cellular Component	endosome	Interproscan
GO:0005802 all species →	Cellular Component	trans-Golgi network	Interproscan
GO:0005886 all species →	Cellular Component	plasma membrane	Interproscan
GO:0007030 all species →	Biological Process	Golgi organization	Interproscan
GO:0007032 all species →	Biological Process	endosome organization	Interproscan
GO:0046854 all species →	Biological Process	phosphatidylinositol phosphate biosynthetic process	Interproscan
GO:0003677 all species →	Molecular Function	DNA binding	Interproscan
GO:0016491 all species →	Molecular Function	oxidoreductase activity	Interproscan
GO:0016899 all species →	Molecular Function	oxidoreductase activity, acting on the CH-OH group of donors, oxygen as acceptor	Interproscan
GO:0004757 all species →	Molecular Function	sepiapterin reductase (NADP+) activity	Interproscan
GO:0006729 all species →	Biological Process	tetrahydrobiopterin biosynthetic process	Interproscan
GO:0009055 all species →	Molecular Function	electron transfer activity	Interproscan
GO:0009061 all species →	Biological Process	anaerobic respiration	Interproscan
GO:0030151 all species →	Molecular Function	molybdenum ion binding	Interproscan
GO:0043546 all species →	Molecular Function	molybdopterin cofactor binding	Interproscan
GO:0004867 all species →	Molecular Function	serine-type endopeptidase inhibitor activity	Interproscan
GO:0005515 all species →	Molecular Function	protein binding	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
K00072	SPR; sepiapterin reductase	EC:1.1.1.153	Exosome	ko04147	deepkoala
K26063	ydiJ; (R)-2-hydroxyglutarate dehydrogenase	EC:1.1.-.-	Lysine degradation	ko00310	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 →