Gene detail

Detailed information of g96.t1 in Calvadosia cruxmelitensis

Genomic Location: not available for this species
NR annotation: WP_274218078.1, transcriptional repressor LexA [Pseudovibrio exalbescens]
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
A0L9E2	LexA repressor OS=Magnetococcus marinus (strain ATCC BAA-1437 / JCM 17883 / MC-1) OX=156889 GN=lexA PE=3 SV=1
Q314F2	LexA repressor OS=Oleidesulfovibrio alaskensis (strain ATCC BAA-1058 / DSM 17464 / G20) OX=207559 GN=lexA PE=3 SV=1
A4XL42	LexA repressor OS=Caldicellulosiruptor saccharolyticus (strain ATCC 43494 / DSM 8903 / Tp8T 6331) OX=351627 GN=lexA PE=3 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0000001 (this species only) · gene tree & orthology
Orthogroup (gene family)	OG0000011 (this species only) · gene tree & orthology
Orthogroup (gene family)	OG0000389 (this species only) · gene tree & orthology
Orthogroup (gene family)	OG0000484 (this species only) · gene tree & orthology
Orthogroup (gene family)	OG0000629 (this species only) · gene tree & orthology
Orthogroup (gene family)	OG0003400 (this species only) · gene tree & orthology
Orthogroup (gene family)	OG0004124 (this species only) · gene tree & orthology
Orthogroup (gene family)	OG0004549 (this species only) · gene tree & orthology
Orthogroup (gene family)	OG0006623 (this species only) · gene tree & orthology
Orthogroup (gene family)	OG0017433 (this species only) · gene tree & orthology
Orthogroup (gene family)	OG0018805 (this species only) · gene tree & orthology
Orthogroup (gene family)	OG0023477 (this species only) · gene tree & orthology
Transcription factor family	Fork_head · all TF in this species

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF01726 all species →	LexA_DNA_bind	LexA DNA binding domain	Domain	Interproscan
PF00717 all species →	Peptidase_S24	Peptidase S24-like	Domain	Interproscan
PF00250 all species →	Forkhead	Forkhead domain	Domain	Interproscan
PF00017 all species →	SH2	SH2 domain	Domain	Interproscan
PF00071 all species →	Ras	Ras family	Domain	Interproscan
PF00098 all species →	zf-CCHC	Zinc knuckle	Domain	Interproscan
PF13650 all species →	Asp_protease_2	Aspartyl protease	Domain	Interproscan
PF00005 all species →	ABC_tran	ABC transporter	Domain	Interproscan
PF01426 all species →	BAH	BAH domain	Domain	Interproscan
PF02574 all species →	S-methyl_trans	Homocysteine S-methyltransferase	Family	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR043128 all species →	Homologous_superfamily	Reverse transcriptase/Diguanylate cyclase domain	Interproscan
IPR050951 all species →	Family	Retrovirus-related Pol polyprotein	Interproscan
IPR043502 all species →	Homologous_superfamily	DNA/RNA polymerase superfamily	Interproscan
IPR006199 all species →	Domain	LexA repressor, DNA-binding domain	Interproscan
IPR006200 all species →	Family	Transcription regulator LexA	Interproscan
IPR015927 all species →	Domain	Peptidase S24/S26A/S26B/S26C	Interproscan
IPR036390 all species →	Homologous_superfamily	Winged helix DNA-binding domain superfamily	Interproscan
IPR036286 all species →	Homologous_superfamily	LexA/Signal peptidase-like superfamily	Interproscan
IPR039418 all species →	Domain	LexA-like	Interproscan
IPR006197 all species →	Family	Peptidase S24, LexA-like	Interproscan
IPR050077 all species →	Family	LexA repressor	Interproscan
IPR036388 all species →	Homologous_superfamily	Winged helix-like DNA-binding domain superfamily	Interproscan
IPR001766 all species →	Domain	Fork head domain	Interproscan
IPR050211 all species →	Family	Forkhead box domain-containing protein	Interproscan
IPR000980 all species →	Domain	SH2 domain	Interproscan
IPR036860 all species →	Homologous_superfamily	SH2 domain superfamily	Interproscan
IPR051184 all species →	Family	Tyrosine-phosphorylated adapter molecule	Interproscan
IPR025958 all species →	Family	SID1 transmembrane family	Interproscan
IPR051065 all species →	Family	Ras-related small GTPase	Interproscan
IPR001806 all species →	Family	Small GTPase	Interproscan
IPR027417 all species →	Homologous_superfamily	P-loop containing nucleoside triphosphate hydrolase	Interproscan
IPR001878 all species →	Domain	Zinc finger, CCHC-type	Interproscan
IPR021109 all species →	Homologous_superfamily	Aspartic peptidase domain superfamily	Interproscan
IPR036875 all species →	Homologous_superfamily	Zinc finger, CCHC-type superfamily	Interproscan
IPR003439 all species →	Domain	ABC transporter-like, ATP-binding domain	Interproscan
IPR017871 all species →	Conserved_site	ABC transporter-like, conserved site	Interproscan
IPR050086 all species →	Family	Methionine Import ATP-binding	Interproscan
IPR030679 all species →	Family	ABC-type amino acid transport system, ATPase component, HisP-type	Interproscan
IPR001025 all species →	Domain	Bromo adjacent homology (BAH) domain	Interproscan
IPR043151 all species →	Homologous_superfamily	Bromo adjacent homology (BAH) domain superfamily	Interproscan
IPR003726 all species →	Domain	Homocysteine-binding domain	Interproscan
IPR036589 all species →	Homologous_superfamily	Homocysteine-binding domain superfamily	Interproscan
IPR051524 all species →	Family	Betaine-homocysteine S-methyltransferase	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR37984 all species →	PROTEIN CBG26694	Interproscan
PTHR33516 all species →	LEXA REPRESSOR	Interproscan
PTHR11829 all species →	FORKHEAD BOX PROTEIN	Interproscan
PTHR19969 all species →	SH2-SH3 ADAPTOR PROTEIN-RELATED	Interproscan
PTHR12185 all species →	SID1 TRANSMEMBRANE FAMILY MEMEBER	Interproscan
PTHR45704 all species →	RAS-LIKE FAMILY MEMBER 11	Interproscan
PTHR43166 all species →	AMINO ACID IMPORT ATP-BINDING PROTEIN	Interproscan
PTHR46120 all species →	BETAINE--HOMOCYSTEINE S-METHYLTRANSFERASE 1	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0004252 all species →	Molecular Function	serine-type endopeptidase activity	Interproscan
GO:0006508 all species →	Biological Process	proteolysis	Interproscan
GO:0009432 all species →	Biological Process	SOS response	Interproscan
GO:0045892 all species →	Biological Process	negative regulation of DNA-templated transcription	Interproscan
GO:0003677 all species →	Molecular Function	DNA binding	Interproscan
GO:0006355 all species →	Biological Process	regulation of DNA-templated transcription	Interproscan
GO:0003700 all species →	Molecular Function	DNA-binding transcription factor activity	Interproscan
GO:0043565 all species →	Molecular Function	sequence-specific DNA binding	Interproscan
GO:0000978 all species →	Molecular Function	RNA polymerase II cis-regulatory region sequence-specific DNA binding	Interproscan
GO:0000981 all species →	Molecular Function	DNA-binding transcription factor activity, RNA polymerase II-specific	Interproscan
GO:0006357 all species →	Biological Process	regulation of transcription by RNA polymerase II	Interproscan
GO:0009653 all species →	Biological Process	anatomical structure morphogenesis	Interproscan
GO:0030154 all species →	Biological Process	cell differentiation	Interproscan
GO:0007165 all species →	Biological Process	signal transduction	Interproscan
GO:0016477 all species →	Biological Process	cell migration	Interproscan
GO:0030971 all species →	Molecular Function	receptor tyrosine kinase binding	Interproscan
GO:0035591 all species →	Molecular Function	signaling adaptor activity	Interproscan
GO:0003725 all species →	Molecular Function	double-stranded RNA binding	Interproscan
GO:0005764 all species →	Cellular Component	lysosome	Interproscan
GO:0005886 all species →	Cellular Component	plasma membrane	Interproscan
GO:0016020 all species →	Cellular Component	membrane	Interproscan
GO:0050658 all species →	Biological Process	RNA transport	Interproscan
GO:0051033 all species →	Molecular Function	RNA transmembrane transporter activity	Interproscan
GO:0003924 all species →	Molecular Function	GTPase activity	Interproscan
GO:0005525 all species →	Molecular Function	GTP binding	Interproscan
GO:0003676 all species →	Molecular Function	nucleic acid binding	Interproscan
GO:0008270 all species →	Molecular Function	zinc ion binding	Interproscan
GO:0005524 all species →	Molecular Function	ATP binding	Interproscan
GO:0016887 all species →	Molecular Function	ATP hydrolysis activity	Interproscan
GO:0003333 all species →	Biological Process	amino acid transmembrane transport	Interproscan
GO:0015424 all species →	Molecular Function	ABC-type amino acid transporter activity	Interproscan
GO:0003682 all species →	Molecular Function	chromatin binding	Interproscan
GO:0009086 all species →	Biological Process	methionine biosynthetic process	Interproscan
GO:0047150 all species →	Molecular Function	betaine-homocysteine S-methyltransferase 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
K00544	BHMT; betaine-homocysteine S-methyltransferase	EC:2.1.1.5	Cysteine and methionine metabolism	ko00270	deepkoala
K01356	lexA; repressor LexA	EC:3.4.21.88	DNA repair and recombination proteins	ko03400	deepkoala
K02028	ABC.PA.A; polar amino acid transport system ATP-binding protein	EC:7.4.2.1	Transporters	ko02000	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 →