Genomic Location: HOLI00001:5136425...5137330
NR annotation: WP_042121423.1, 30S ribosomal protein S6--L-glutamate ligase [Pseudomonas japonica]
Species Hydra oligactis · all data for this species · gene families
| CDS |
| HOLI00001.g53044.t1 |
| Transcript |
| HOLI00001.g53044.t1 |
| Protein |
| HOLI00001.G53044 |
| UniProt accession | Description |
|---|---|
| Q1IGK6 | Probable alpha-L-glutamate ligase OS=Pseudomonas entomophila (strain L48) OX=384676 GN=rimK PE=3 SV=1 |
| B1JET8 | Probable alpha-L-glutamate ligase OS=Pseudomonas putida (strain W619) OX=390235 GN=rimK PE=3 SV=1 |
| A5VX27 | Probable alpha-L-glutamate ligase OS=Pseudomonas putida (strain ATCC 700007 / DSM 6899 / JCM 31910 / BCRC 17059 / LMG 24140 / F1) OX=351746 GN=rimK PE=3 SV=1 |
| Family type | Membership / link |
|---|---|
| Orthogroup (gene family) | OG0042792 (this species only) · gene tree & orthology |
| Pfam accession | Pfam name | Description | Type | Source |
|---|---|---|---|---|
| PF08443 all species → | RimK | RimK-like ATP-grasp domain | Domain | Interproscan |
| PF18030 all species → | Rimk_N | RimK PreATP-grasp domain | Domain | Interproscan |
| InterPro term | Type | Description | Source |
|---|---|---|---|
| IPR013651 all species → | Domain | ATP-grasp fold, RimK-type | Interproscan |
| IPR013815 all species → | Homologous_superfamily | ATP-grasp fold, subdomain 1 | Interproscan |
| IPR004666 all species → | Family | Ribosomal bS6 modification enzyme RimK/Lysine biosynthesis enzyme LysX | Interproscan |
| IPR011761 all species → | Domain | ATP-grasp fold | Interproscan |
| IPR023533 all species → | Family | Ribosomal protein bS6-L-glutamate ligase | Interproscan |
| IPR041107 all species → | Domain | RimK, preATP-grasp domain | Interproscan |
| PANTHER term | Description | Source |
|---|---|---|
| PTHR21621 all species → | RIBOSOMAL PROTEIN S6 MODIFICATION PROTEIN | Interproscan |
| GO term | Category | Description | Source |
|---|---|---|---|
| GO:0005524 all species → | Molecular Function | ATP binding | Interproscan |
| GO:0005737 all species → | Cellular Component | cytoplasm | Interproscan |
| GO:0009432 all species → | Biological Process | SOS response | Interproscan |
| GO:0016879 all species → | Molecular Function | ligase activity, forming carbon-nitrogen bonds | Interproscan |
| GO:0018169 all species → | Molecular Function | ribosomal S6-glutamic acid ligase activity | Interproscan |
| GO:0018410 all species → | Biological Process | C-terminal protein amino acid modification | Interproscan |
| GO:0036211 all species → | Biological Process | protein modification process | Interproscan |
| GO:0046872 all species → | Molecular Function | metal ion binding | Interproscan |
| KO | Enzyme | Enzyme ID | Pathway | Map ID | Source |
|---|---|---|---|---|---|
| K05844 | rimK; ribosomal protein S6--L-glutamate ligase | EC:6.3.2.- | Ribosome biogenesis | ko03009 | deepkoala |
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.
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.
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.
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. | template found | open → |
| 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. | template found | open → |
| 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 → |
