Genomic Location: QPEY01000551.1:119278...120477
NR annotation: WP_250529642.1, pyrroloquinoline quinone biosynthesis protein PqqE [Caballeronia sp. ATUFL_F1_KS4A]
Species Hydra viridissima · all data for this species · gene families
| CDS |
| BRAKERKRET00000024796 |
| Transcript |
| BRAKERKRET00000024796 |
| Protein |
| BRAKERKREP00000024796.1 |
| UniProt accession | Description |
|---|---|
| Q608P0 | PqqA peptide cyclase OS=Methylococcus capsulatus (strain ATCC 33009 / NCIMB 11132 / Bath) OX=243233 GN=pqqE PE=3 SV=1 |
| Q4K4U8 | PqqA peptide cyclase OS=Pseudomonas fluorescens (strain ATCC BAA-477 / NRRL B-23932 / Pf-5) OX=220664 GN=pqqE PE=3 SV=1 |
| Q88A84 | PqqA peptide cyclase OS=Pseudomonas syringae pv. tomato (strain ATCC BAA-871 / DC3000) OX=223283 GN=pqqE PE=3 SV=1 |
| Family type | Membership / link |
|---|---|
| Orthogroup (gene family) | OG0050202 (this species only) · gene tree & orthology |
| Pfam accession | Pfam name | Description | Type | Source |
|---|---|---|---|---|
| PF04055 all species → | Radical_SAM | Radical SAM superfamily | Domain | Interproscan |
| PF13186 all species → | SPASM | Iron-sulfur cluster-binding domain | Domain | Interproscan |
| InterPro term | Type | Description | Source |
|---|---|---|---|
| IPR011843 all species → | Family | Coenzyme PQQ biosynthesis protein E, bacteria | Interproscan |
| IPR007197 all species → | Domain | Radical SAM | Interproscan |
| IPR017200 all species → | Family | Coenzyme PQQ synthesis protein E-like | Interproscan |
| IPR050377 all species → | Family | Radical SAM superfamily enzymes | Interproscan |
| IPR013785 all species → | Homologous_superfamily | Aldolase-type TIM barrel | Interproscan |
| IPR023885 all species → | Domain | 4Fe4S-binding SPASM domain | Interproscan |
| IPR006638 all species → | Domain | Elp3/MiaA/NifB-like, radical SAM core domain | Interproscan |
| PANTHER term | Description | Source |
|---|---|---|
| PTHR11228 all species → | RADICAL SAM DOMAIN PROTEIN | Interproscan |
| GO term | Category | Description | Source |
|---|---|---|---|
| GO:0018189 all species → | Biological Process | pyrroloquinoline quinone biosynthetic process | Interproscan |
| GO:0051539 all species → | Molecular Function | 4 iron, 4 sulfur cluster binding | Interproscan |
| GO:0003824 all species → | Molecular Function | catalytic activity | Interproscan |
| GO:0051536 all species → | Molecular Function | iron-sulfur cluster binding | Interproscan |
| KO | Enzyme | Enzyme ID | Pathway | Map ID | Source |
|---|---|---|---|---|---|
| K06139 | pqqE; PqqA peptide cyclase | EC:1.21.98.4 | Enzymes with EC numbers | - | deepkoala |
Transcript abundance of BRAKERKREP00000024796.1 across 29 RNA-seq samples of Hydra viridissima. Values are TPM (transcripts per million) from the StringTie quantification; one bar is one sample, grouped and coloured by condition, sorted by expression within each group.
| Condition | Samples | TPM > 0 | Mean TPM | Max TPM | Mean, relative to max |
|---|---|---|---|---|---|
| whole body | 18 | 1 | 0.04 | 0.79 | |
| Whole | 6 | 6 | 2.20 | 3.79 | |
| aposymbioic hydra M9 strain · aposymbioic hydra rep1 | 1 | 1 | 0.79 | 0.79 | |
| aposymbioic hydra M9 strain · aposymbioic hydra rep2 | 1 | 1 | 0.03 | 0.03 | |
| symbioic hydra M9 strain · symbioic hydra rep1 | 1 | 1 | 0.02 | 0.02 | |
| symbioic hydra M9 strain · symbioic hydra rep2 | 1 | 0 | 0.00 | 0.00 | |
| unannotated | 1 | 0 | 0.00 | 0.00 |
| SRA run | Condition | Tissue | Developmental stage | Treatment | Study | TPM |
|---|---|---|---|---|---|---|
| SRR21134060 | whole body | whole body | not recorded | not recorded | SRP392977 | 0.79 |
| SRR21134050 | whole body | whole body | not recorded | not recorded | SRP392977 | 0.00 |
| SRR21134051 | whole body | whole body | not recorded | not recorded | SRP392977 | 0.00 |
| SRR21134052 | whole body | whole body | not recorded | not recorded | SRP392977 | 0.00 |
| SRR21134053 | whole body | whole body | not recorded | not recorded | SRP392977 | 0.00 |
| SRR21134054 | whole body | whole body | not recorded | not recorded | SRP392977 | 0.00 |
| SRR21134055 | whole body | whole body | not recorded | not recorded | SRP392977 | 0.00 |
| SRR21134056 | whole body | whole body | not recorded | not recorded | SRP392977 | 0.00 |
| SRR21134057 | whole body | whole body | not recorded | not recorded | SRP392977 | 0.00 |
| SRR21134058 | whole body | whole body | not recorded | not recorded | SRP392977 | 0.00 |
| SRR21134059 | whole body | whole body | not recorded | not recorded | SRP392977 | 0.00 |
| SRR21134061 | whole body | whole body | not recorded | not recorded | SRP392977 | 0.00 |
| SRR21134062 | whole body | whole body | not recorded | not recorded | SRP392977 | 0.00 |
| SRR21134063 | whole body | whole body | not recorded | not recorded | SRP392977 | 0.00 |
| SRR21134064 | whole body | whole body | not recorded | not recorded | SRP392977 | 0.00 |
| SRR21134065 | whole body | whole body | not recorded | not recorded | SRP392977 | 0.00 |
| SRR21134066 | whole body | whole body | not recorded | not recorded | SRP392977 | 0.00 |
| SRR21134067 | whole body | whole body | not recorded | not recorded | SRP392977 | 0.00 |
| SRR10058803 | Whole | Whole | not recorded | not recorded | SRP220397 | 3.79 |
| SRR10058806 | Whole | Whole | not recorded | not recorded | SRP220397 | 2.84 |
| SRR10058807 | Whole | Whole | not recorded | not recorded | SRP220397 | 2.74 |
| SRR10058805 | Whole | Whole | not recorded | not recorded | SRP220397 | 2.56 |
| SRR10058804 | Whole | Whole | not recorded | not recorded | SRP220397 | 0.65 |
| SRR10058802 | Whole | Whole | not recorded | not recorded | SRP220397 | 0.59 |
| DRR048593 | aposymbioic hydra M9 strain · aposymbioic hydra rep1 | not recorded | not recorded | aposymbioic hydra rep1 | DRP003902 | 0.79 |
| DRR048594 | aposymbioic hydra M9 strain · aposymbioic hydra rep2 | not recorded | not recorded | aposymbioic hydra rep2 | DRP003902 | 0.03 |
| DRR048595 | symbioic hydra M9 strain · symbioic hydra rep1 | not recorded | not recorded | symbioic hydra rep1 | DRP003902 | 0.02 |
| DRR048596 | symbioic hydra M9 strain · symbioic hydra rep2 | not recorded | not recorded | symbioic hydra rep2 | DRP003902 | 0.00 |
| ERR13389755 | unannotated | not recorded | not recorded | not recorded | ERP162636 | 0.00 |
Source: CnidoSite RNA-seq expression matrices (HVIRI_TPM,
StringTie quantification over 29 runs), joined to SRA sample
metadata. Samples whose tissue/treatment is not recorded in the source metadata are grouped
by the descriptor carried in the expression matrix itself.
Genes whose expression across the transcriptome samples of Hydra viridissima 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.
| Direction | Partners | Most correlated partner | PCC |
|---|---|---|---|
| Positively correlated | 4 | BRAKERKREP00000001291.1 | 0.976938242967315 |
| Negatively correlated | 3 | BRAKERKREP00000024112.1 | -0.533411853579285 |
Open this gene in Network Analysis → The network opens with the gene already entered and both directions selected. There you can add up to 9 more genes, switch between the positive and negative network, and export the edge list.
Whether this gene can be visualised in the single-cell atlases of Hydra viridissima, 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. | ready | open → |
| 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 → |
