Gene detail

Detailed information of g871.t1 in Calvadosia cruxmelitensis

Genomic Location: not available for this species
NR annotation: MBL0691412.1, PBP1A family penicillin-binding protein [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
Q1RKC5	Penicillin-binding protein 1A OS=Rickettsia bellii (strain RML369-C) OX=336407 GN=mrcA PE=3 SV=1
Q68VU2	Penicillin-binding protein 1A OS=Rickettsia typhi (strain ATCC VR-144 / Wilmington) OX=257363 GN=mrcA PE=3 SV=1
Q9KNU5	Penicillin-binding protein 1A OS=Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961) OX=243277 GN=mrcA PE=3 SV=2

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0000005 (this species only) · gene tree & orthology
Orthogroup (gene family)	OG0000033 (this species only) · gene tree & orthology
Orthogroup (gene family)	OG0000065 (this species only) · gene tree & orthology
Orthogroup (gene family)	OG0000556 (this species only) · gene tree & orthology
Orthogroup (gene family)	OG0002097 (this species only) · gene tree & orthology
Orthogroup (gene family)	OG0002339 (this species only) · gene tree & orthology
Orthogroup (gene family)	OG0002416 (this species only) · gene tree & orthology
Orthogroup (gene family)	OG0003932 (this species only) · gene tree & orthology
Orthogroup (gene family)	OG0005224 (this species only) · gene tree & orthology
Orthogroup (gene family)	OG0007481 (this species only) · gene tree & orthology
Orthogroup (gene family)	OG0008567 (this species only) · gene tree & orthology
Orthogroup (gene family)	OG0017737 (this species only) · gene tree & orthology
Orthogroup (gene family)	OG0083662 (this species only) · gene tree & orthology

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF10274 all species →	ParcG	Parkin co-regulated protein	Repeat	Interproscan
PF21056 all species →	ZSWIM1-3_RNaseH-like	Zinc finger SWIM domain-containing protein 1/3, RNaseH-like domain	Domain	Interproscan
PF20784 all species →	DUF5575_C	DUF5575 C-terminal domain	Domain	Interproscan
PF02127 all species →	Peptidase_M18	Aminopeptidase I zinc metalloprotease (M18)	Family	Interproscan
PF07690 all species →	MFS_1	Major Facilitator Superfamily	Family	Interproscan
PF00912 all species →	Transgly	Transglycosylase	Family	Interproscan
PF04079 all species →	SMC_ScpB	Segregation and condensation complex subunit ScpB	Family	Interproscan
PF01472 all species →	PUA	PUA domain	Family	Interproscan
PF03938 all species →	OmpH	Outer membrane protein (OmpH-like)	Domain	Interproscan
PF17092 all species →	PCB_OB	Penicillin-binding protein OB-like domain	Family	Interproscan
PF00905 all species →	Transpeptidase	Penicillin binding protein transpeptidase domain	Domain	Interproscan
PF00696 all species →	AA_kinase	Amino acid kinase family	Family	Interproscan
PF13409 all species →	GST_N_2	Glutathione S-transferase, N-terminal domain	Domain	Interproscan
PF09730 all species →	BicD	Microtubule-associated protein Bicaudal-D	Coiled-coil	Interproscan
PF05454 all species →	DAG1	Dystroglycan (Dystrophin-associated glycoprotein 1)	Family	Interproscan
PF14538 all species →	Raptor_N	Raptor N-terminal CASPase like domain	Domain	Interproscan
PF00078 all species →	RVT_1	Reverse transcriptase (RNA-dependent DNA polymerase)	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR019399 all species →	Family	Parkin co-regulated protein	Interproscan
IPR016024 all species →	Homologous_superfamily	Armadillo-type fold	Interproscan
IPR048324 all species →	Domain	ZSWIM1/3, RNaseH-like domain	Interproscan
IPR007527 all species →	Domain	Zinc finger, SWIM-type	Interproscan
IPR049218 all species →	Domain	DUF5575, C-terminal domain	Interproscan
IPR052579 all species →	Family	Zinc finger SWIM domain-containing protein	Interproscan
IPR001948 all species →	Family	Peptidase M18	Interproscan
IPR023358 all species →	Homologous_superfamily	Peptidase M18, domain 2	Interproscan
IPR002478 all species →	Domain	PUA domain	Interproscan
IPR005715 all species →	Family	Glutamate 5-kinase/delta-1-pyrroline-5-carboxylate synthase	Interproscan
IPR005632 all species →	Family	Chaperone protein Skp	Interproscan
IPR011701 all species →	Family	Major facilitator superfamily	Interproscan
IPR001264 all species →	Domain	Glycosyl transferase, family 51	Interproscan
IPR024930 all species →	Homologous_superfamily	Skp domain superfamily	Interproscan
IPR012338 all species →	Homologous_superfamily	Beta-lactamase/transpeptidase-like	Interproscan
IPR001057 all species →	Family	Glutamate/acetylglutamate kinase	Interproscan
IPR036393 all species →	Homologous_superfamily	Acetylglutamate kinase-like superfamily	Interproscan
IPR050396 all species →	Family	Glycosyltransferase 51/Transpeptidase	Interproscan
IPR005234 all species →	Family	Chromosome segregation/condensation protein ScpB	Interproscan
IPR023346 all species →	Homologous_superfamily	Lysozyme-like domain superfamily	Interproscan
IPR036950 all species →	Homologous_superfamily	Penicillin binding protein transglycosylase domain	Interproscan
IPR041739 all species →	Domain	Glutamate-5-kinase domain	Interproscan
IPR036974 all species →	Homologous_superfamily	PUA domain superfamily	Interproscan
IPR031376 all species →	Domain	Penicillin-binding protein, OB-like domain	Interproscan
IPR015947 all species →	Homologous_superfamily	PUA-like superfamily	Interproscan
IPR036388 all species →	Homologous_superfamily	Winged helix-like DNA-binding domain superfamily	Interproscan
IPR001460 all species →	Domain	Penicillin-binding protein, transpeptidase	Interproscan
IPR001048 all species →	Domain	Aspartate/glutamate/uridylate kinase	Interproscan
IPR036259 all species →	Homologous_superfamily	MFS transporter superfamily	Interproscan
IPR016639 all species →	Family	Glutathione S-transferase Omega/GSH	Interproscan
IPR004045 all species →	Domain	Glutathione S-transferase, N-terminal	Interproscan
IPR036249 all species →	Homologous_superfamily	Thioredoxin-like superfamily	Interproscan
IPR018477 all species →	Family	Bicaudal-D protein	Interproscan
IPR015919 all species →	Homologous_superfamily	Cadherin-like superfamily	Interproscan
IPR013783 all species →	Homologous_superfamily	Immunoglobulin-like fold	Interproscan
IPR030398 all species →	Domain	DG-type SEA domain	Interproscan
IPR006644 all species →	Domain	Dystroglycan-type cadherin-like	Interproscan
IPR027468 all species →	Homologous_superfamily	Alpha-dystroglycan domain 2	Interproscan
IPR008465 all species →	Domain	Dystroglycan, C-terminal	Interproscan
IPR029347 all species →	Domain	Raptor, N-terminal CASPase-like domain	Interproscan
IPR004083 all species →	Family	Regulatory associated protein of TOR	Interproscan
IPR000477 all species →	Domain	Reverse transcriptase domain	Interproscan
IPR043502 all species →	Homologous_superfamily	DNA/RNA polymerase superfamily	Interproscan
IPR027417 all species →	Homologous_superfamily	P-loop containing nucleoside triphosphate hydrolase	Interproscan
IPR013395 all species →	Family	CRISPR-associated Cas3, Yersinia-type	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR21207 all species →	PARKIN COREGULATED GENE PROTEIN PARK2 COREGULATED	Interproscan
PTHR31569 all species →	SWIM-TYPE DOMAIN-CONTAINING PROTEIN	Interproscan
PTHR28570 all species →	ASPARTYL AMINOPEPTIDASE	Interproscan
PTHR32282 all species →	BINDING PROTEIN TRANSPEPTIDASE, PUTATIVE-RELATED	Interproscan
PTHR32419 all species →	GLUTATHIONYL-HYDROQUINONE REDUCTASE	Interproscan
PTHR31233 all species →	BICAUDAL D FAMILY MEMBER	Interproscan
PTHR21559 all species →	DYSTROGLYCAN-RELATED	Interproscan
PTHR12848 all species →	REGULATORY-ASSOCIATED PROTEIN OF MTOR	Interproscan
PTHR47027 all species →	REVERSE TRANSCRIPTASE DOMAIN-CONTAINING PROTEIN	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0030544 all species →	Molecular Function	Hsp70 protein binding	Interproscan
GO:0051879 all species →	Molecular Function	Hsp90 protein binding	Interproscan
GO:0060548 all species →	Biological Process	obsolete negative regulation of cell death	Interproscan
GO:0008270 all species →	Molecular Function	zinc ion binding	Interproscan
GO:0004177 all species →	Molecular Function	aminopeptidase activity	Interproscan
GO:0006508 all species →	Biological Process	proteolysis	Interproscan
GO:0003723 all species →	Molecular Function	RNA binding	Interproscan
GO:0005737 all species →	Cellular Component	cytoplasm	Interproscan
GO:0006561 all species →	Biological Process	proline biosynthetic process	Interproscan
GO:0051082 all species →	Molecular Function	unfolded protein binding	Interproscan
GO:0022857 all species →	Molecular Function	transmembrane transporter activity	Interproscan
GO:0055085 all species →	Biological Process	transmembrane transport	Interproscan
GO:0005524 all species →	Molecular Function	ATP binding	Interproscan
GO:0016301 all species →	Molecular Function	kinase activity	Interproscan
GO:0008658 all species →	Molecular Function	penicillin binding	Interproscan
GO:0008955 all species →	Molecular Function	peptidoglycan glycosyltransferase activity	Interproscan
GO:0009252 all species →	Biological Process	peptidoglycan biosynthetic process	Interproscan
GO:0046677 all species →	Biological Process	response to antibiotic	Interproscan
GO:0051304 all species →	Biological Process	chromosome separation	Interproscan
GO:0004364 all species →	Molecular Function	glutathione transferase activity	Interproscan
GO:0008093 all species →	Molecular Function	cytoskeletal anchor activity	Interproscan
GO:0070840 all species →	Molecular Function	dynein complex binding	Interproscan
GO:0005509 all species →	Molecular Function	calcium ion binding	Interproscan
GO:0016020 all species →	Cellular Component	membrane	Interproscan
GO:0002009 all species →	Biological Process	morphogenesis of an epithelium	Interproscan
GO:0007411 all species →	Biological Process	axon guidance	Interproscan
GO:0016011 all species →	Cellular Component	dystroglycan complex	Interproscan
GO:0016203 all species →	Biological Process	muscle attachment	Interproscan
GO:0021675 all species →	Biological Process	nerve development	Interproscan
GO:0042383 all species →	Cellular Component	sarcolemma	Interproscan
GO:0043236 all species →	Molecular Function	laminin binding	Interproscan
GO:0016010 all species →	Cellular Component	dystrophin-associated glycoprotein complex	Interproscan
GO:0009267 all species →	Biological Process	cellular response to starvation	Interproscan
GO:0010506 all species →	Biological Process	regulation of autophagy	Interproscan
GO:0030307 all species →	Biological Process	positive regulation of cell growth	Interproscan
GO:0030674 all species →	Molecular Function	protein-macromolecule adaptor activity	Interproscan
GO:0031929 all species →	Biological Process	TOR signaling	Interproscan
GO:0031931 all species →	Cellular Component	TORC1 complex	Interproscan
GO:0038202 all species →	Biological Process	TORC1 signaling	Interproscan
GO:0071230 all species →	Biological Process	cellular response to amino acid stimulus	Interproscan
GO:0071902 all species →	Biological Process	positive regulation of protein serine/threonine kinase 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
K18739	BICD; protein bicaudal D	-	Membrane trafficking	ko04131	deepkoala
K26163	PACRG; parkin coregulated gene protein	-	Ubiquitin system	ko04121	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 →