Detailed information of HOLI00002.G17699 in Hydra oligactis

Genomic Location: HOLI00002:478844...479551
NR annotation: MBI3517857.1, 4-hydroxy-tetrahydrodipicolinate reductase [Bacteroidota bacterium]
Species Hydra oligactis · all data for this species · gene families


 Gene Structure
More details in JBrowse  Sequence
CDS
Transcript
Protein
 UniProt (Swiss-Prot top hit)
UniProt accessionDescription
A0LZI44-hydroxy-tetrahydrodipicolinate reductase OS=Christiangramia forsetii (strain DSM 17595 / CGMCC 1.15422 / KT0803) OX=411154 GN=dapB PE=3 SV=1
B3QYM84-hydroxy-tetrahydrodipicolinate reductase OS=Chloroherpeton thalassium (strain ATCC 35110 / GB-78) OX=517418 GN=dapB PE=3 SV=1
Q5F5Y74-hydroxy-tetrahydrodipicolinate reductase OS=Neisseria gonorrhoeae (strain ATCC 700825 / FA 1090) OX=242231 GN=dapB PE=1 SV=1
 Pfam domain
Pfam accessionPfam nameDescriptionTypeSource
PF05173
all species →		DapB_CDihydrodipicolinate reductase, C-terminusDomainInterproscan
PF01113
all species →		DapB_NDihydrodipicolinate reductase, N-terminusDomainInterproscan

 InterPro
InterPro termTypeDescriptionSource
IPR022663
all species →		DomainDihydrodipicolinate reductase, C-terminalInterproscan
IPR036291
all species →		Homologous_superfamilyNAD(P)-binding domain superfamilyInterproscan
IPR023940
all species →		FamilyDihydrodipicolinate reductaseInterproscan
IPR000846
all species →		DomainDihydrodipicolinate reductase, N-terminalInterproscan

 PANTHER
PANTHER termDescriptionSource
PTHR20836
all species →		DIHYDRODIPICOLINATE REDUCTASEInterproscan

 Gene Ontology
GO termCategoryDescriptionSource
GO:0008839
all species →		Molecular Function4-hydroxy-tetrahydrodipicolinate reductaseInterproscan
GO:0009089
all species →		Biological Processlysine biosynthetic process via diaminopimelateInterproscan
GO:0005829
all species →		Cellular ComponentcytosolInterproscan
GO:0019877
all species →		Biological Processdiaminopimelate biosynthetic processInterproscan

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
KOEnzymeEnzyme IDPathwayMap IDSource
K00215dapB; 4-hydroxy-tetrahydrodipicolinate reductaseEC:1.17.1.8
Monobactam biosynthesisko00261deepkoala

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 Hydra oligactis 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 Hydra oligactis, 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.

AnalysisWhat it doesStatus
Primer designDesign PCR / qPCR primers on this gene’s sequence with the published primer3 settings. Opens with the primers already computed.template foundopen →
BLASTSearch this gene’s sequence against the CnidoSite BLAST databases. The query is filled in and the species’ database is preselected — press Run to start.template foundopen →
Expression heatmapDraw 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 / orthogroupLook 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 analysisStart a gene-set enrichment analysis with this gene as the seed list. Add more genes on that page before running it.open →
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