Gene detail

Detailed information of g879.t1 in Calvadosia cruxmelitensis

Genomic Location: not available for this species
NR annotation: MBU2511707.1, penicillin-binding protein 2 [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
D0C8Z9	Peptidoglycan D,D-transpeptidase MrdA OS=Acinetobacter baumannii (strain ATCC 19606 / DSM 30007 / JCM 6841 / CCUG 19606 / CIP 70.34 / NBRC 109757 / NCIMB 12457 / NCTC 12156 / 81) OX=575584 GN=mrdA PE=1 SV=1
Q03524	Stage V sporulation protein D OS=Bacillus subtilis (strain 168) OX=224308 GN=spoVD PE=1 SV=3
P08149	Probable peptidoglycan D,D-transpeptidase PenA OS=Neisseria gonorrhoeae OX=485 GN=penA PE=1 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0001552 (this species only) · gene tree & orthology
Orthogroup (gene family)	OG0002085 (this species only) · gene tree & orthology
Orthogroup (gene family)	OG0002116 (this species only) · gene tree & orthology
Orthogroup (gene family)	OG0003257 (this species only) · gene tree & orthology
Orthogroup (gene family)	OG0003446 (this species only) · gene tree & orthology
Orthogroup (gene family)	OG0007636 (this species only) · gene tree & orthology
Orthogroup (gene family)	OG0008033 (this species only) · gene tree & orthology
Orthogroup (gene family)	OG0008042 (this species only) · gene tree & orthology
Orthogroup (gene family)	OG0013938 (this species only) · gene tree & orthology
Orthogroup (gene family)	OG0061752 (this species only) · gene tree & orthology
Orthogroup (gene family)	OG0061785 (this species only) · gene tree & orthology

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF04136 all species →	COG3_N	Conserved oligomeric Golgi complex subunit 3, N-terminal	Repeat	Interproscan
PF06032 all species →	DUF917	Protein of unknown function (DUF917), N-terminal	Domain	Interproscan
PF20906 all species →	DUF917_C	Protein of unknown function DUF917, C-terminal	Domain	Interproscan
PF12796 all species →	Ank_2	Ankyrin repeats (3 copies)	Repeat	Interproscan
PF03717 all species →	PBP_dimer	Penicillin-binding Protein dimerisation domain	Domain	Interproscan
PF00905 all species →	Transpeptidase	Penicillin binding protein transpeptidase domain	Domain	Interproscan
PF00412 all species →	LIM	LIM domain	Domain	Interproscan
PF12130 all species →	bMERB_dom	Bivalent Mical/EHBP Rab binding domain	Domain	Interproscan
PF14770 all species →	TMEM18	Transmembrane protein 18	Family	Interproscan
PF03874 all species →	RNA_pol_Rpb4	RNA polymerase Rpb4	Family	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR048320 all species →	Domain	Conserved oligomeric Golgi complex subunit 3, N-terminal	Interproscan
IPR007265 all species →	Family	Conserved oligomeric Golgi complex, subunit 3	Interproscan
IPR027479 all species →	Homologous_superfamily	DUF917, N-terminal domain superfamily	Interproscan
IPR010318 all species →	Domain	DUF917, N-terminal domain	Interproscan
IPR024071 all species →	Homologous_superfamily	DUF917, C-terminal domain superfamily	Interproscan
IPR048350 all species →	Domain	DUF917, C-terminal domain	Interproscan
IPR002110 all species →	Repeat	Ankyrin repeat	Interproscan
IPR036770 all species →	Homologous_superfamily	Ankyrin repeat-containing domain superfamily	Interproscan
IPR005311 all species →	Domain	Penicillin-binding protein, dimerisation domain	Interproscan
IPR012338 all species →	Homologous_superfamily	Beta-lactamase/transpeptidase-like	Interproscan
IPR050515 all species →	Family	Bacterial Transpeptidases and Beta-Lactamases	Interproscan
IPR001460 all species →	Domain	Penicillin-binding protein, transpeptidase	Interproscan
IPR036138 all species →	Homologous_superfamily	Penicillin-binding protein, dimerisation domain superfamily	Interproscan
IPR017790 all species →	Family	Penicillin-binding protein 2	Interproscan
IPR001781 all species →	Domain	Zinc finger, LIM-type	Interproscan
IPR022735 all species →	Domain	bMERB domain	Interproscan
IPR052771 all species →	Family	Neurotrophin-activated signaling adaptor	Interproscan
IPR000836 all species →	Domain	Phosphoribosyltransferase domain	Interproscan
IPR023031 all species →	Family	Orotate phosphoribosyltransferase	Interproscan
IPR004467 all species →	Domain	Orotate phosphoribosyl transferase domain	Interproscan
IPR029057 all species →	Homologous_superfamily	Phosphoribosyltransferase-like	Interproscan
IPR026721 all species →	Family	Transmembrane protein 18	Interproscan
IPR028994 all species →	Homologous_superfamily	Integrin alpha, N-terminal	Interproscan
IPR010997 all species →	Homologous_superfamily	HRDC-like superfamily	Interproscan
IPR045222 all species →	Family	DNA-directed RNA polymerase II subunit Rpb4-like	Interproscan
IPR005574 all species →	Family	RNA polymerase subunit Rpb4/RPC9	Interproscan
IPR038324 all species →	Homologous_superfamily	Rpb4/RPC9 superfamily	Interproscan
IPR006590 all species →	Domain	RNA polymerase Rpb4/RPC9, core	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR13302 all species →	CONSERVED OLIGOMERIC GOLGI COMPLEX COMPONENT 3	Interproscan
PTHR30627 all species →	PEPTIDOGLYCAN D,D-TRANSPEPTIDASE	Interproscan
PTHR24206 all species →	OS06G0237300 PROTEIN	Interproscan
PTHR24116 all species →	KINASE D-INTERACTING SUBSTRATE OF 220 KDA	Interproscan
PTHR19278 all species →	OROTATE PHOSPHORIBOSYLTRANSFERASE	Interproscan
PTHR46580 all species →	SENSOR KINASE-RELATED	Interproscan
PTHR21297 all species →	DNA-DIRECTED RNA POLYMERASE II	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0005801 all species →	Cellular Component	cis-Golgi network	Interproscan
GO:0006886 all species →	Biological Process	intracellular protein transport	Interproscan
GO:0006891 all species →	Biological Process	intra-Golgi vesicle-mediated transport	Interproscan
GO:0007030 all species →	Biological Process	Golgi organization	Interproscan
GO:0016020 all species →	Cellular Component	membrane	Interproscan
GO:0017119 all species →	Cellular Component	Golgi transport complex	Interproscan
GO:0005515 all species →	Molecular Function	protein binding	Interproscan
GO:0008658 all species →	Molecular Function	penicillin binding	Interproscan
GO:0005887 all species →	Cellular Component	plasma membrane	Interproscan
GO:0071555 all species →	Biological Process	cell wall organization	Interproscan
GO:0071972 all species →	Molecular Function	peptidoglycan L,D-transpeptidase activity	Interproscan
GO:0009002 all species →	Molecular Function	serine-type D-Ala-D-Ala carboxypeptidase activity	Interproscan
GO:0009252 all species →	Biological Process	peptidoglycan biosynthetic process	Interproscan
GO:0005886 all species →	Cellular Component	plasma membrane	Interproscan
GO:0015629 all species →	Cellular Component	actin cytoskeleton	Interproscan
GO:0051015 all species →	Molecular Function	actin filament binding	Interproscan
GO:0051017 all species →	Biological Process	actin filament bundle assembly	Interproscan
GO:0019887 all species →	Molecular Function	protein kinase regulator activity	Interproscan
GO:0030165 all species →	Molecular Function	PDZ domain binding	Interproscan
GO:0004588 all species →	Molecular Function	orotate phosphoribosyltransferase activity	Interproscan
GO:0006222 all species →	Biological Process	UMP biosynthetic process	Interproscan
GO:0019856 all species →	Biological Process	pyrimidine nucleobase biosynthetic process	Interproscan
GO:0006221 all species →	Biological Process	pyrimidine nucleotide biosynthetic process	Interproscan
GO:0000166 all species →	Molecular Function	nucleotide binding	Interproscan
GO:0044237 all species →	Biological Process	obsolete cellular metabolic process	Interproscan
GO:0005665 all species →	Cellular Component	RNA polymerase II, core complex	Interproscan
GO:0006367 all species →	Biological Process	transcription initiation at RNA polymerase II promoter	Interproscan
GO:0031369 all species →	Molecular Function	translation initiation factor binding	Interproscan
GO:0034402 all species →	Biological Process	obsolete recruitment of 3'-end processing factors to RNA polymerase II holoenzyme complex	Interproscan
GO:0006352 all species →	Biological Process	DNA-templated transcription initiation	Interproscan
GO:0030880 all species →	Cellular Component	RNA polymerase complex	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
K00762	pyrE; orotate phosphoribosyltransferase	EC:2.4.2.10	Pyrimidine metabolism	ko00240	deepkoala
K03012	RPB4, POLR2D; DNA-directed RNA polymerase II subunit RPB4	-	DNA repair and recombination proteins	ko03400	deepkoala
K05515	mrdA; penicillin-binding protein 2	EC:3.4.16.4	Peptidoglycan biosynthesis and degradation proteins	ko01011	deepkoala
K22145	TMEM18; transmembrane protein 18	-	Transcription factors	ko03000	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 →