Plasmid CP052983.1
Sequence
Nucleotide Information
| Accession | CP052983.1 |
|---|---|
| Description | Staphylococcus epidermidis strain HD25-1 plasmid pHD25-1_2, complete sequence |
| Source | insd |
| Topology | circular |
| Length | 2366 bp |
| GC Content | 0.31 % |
| Created at NCBI | Feb. 9, 2021 |
Host Taxonomy
According to NCBI Taxonomy
| Assigned Host | Staphylococcus epidermidis (1282) |
|---|
Lineage
| Superkingdom | Bacteria (2) |
|---|---|
| Phylum | Bacillota (1239) |
| Class | Bacilli (91061) |
| Order | Bacillales (1385) |
| Family | Staphylococcaceae (90964) |
| Genus | Staphylococcus (1279) |
| Species | Staphylococcus_epidermidis (1282) |
| Strain |
Biosample
Curated Collection Information
| Accession | 14732892 |
|---|
PLASMID INFORMATION
GEOGRAPHICAL INFORMATION
| Original Query | 53.33N;10.1E |
|---|---|
| Original Query Type | coordinates |
| Coordinates (Lat/Lon) | 53.33/10.10 |
| Address | Zum Woldberg, Winsen (Luhe), Harburg, Lower Saxony, 21423, Germany |
ECOSYSTEM
| Original Query | Homo sapiens,nose; prosthetic joint infection |
|---|---|
| Classification | disease,host_associated |
| Host-associated Taxon |
|
DISEASE
| Original Query | Prosthesis Related Infections |
|---|---|
| DOID/SYMP |
|
Visualization
Plasmids from same Biosample
Similar Plasmids
based on Mash distance
Plasmid Visualization
Grays
Blues
Purples
Reds
Oranges
Greens
100
Hex
R
G
B
| Source | Element Name | Display | Sequence | Favorite |
|---|---|---|---|---|
| rgi | ErmC | copy | ||
| rgi | ErmC | copy | ||
| PGAG | 23S rRNA (adenine(2058)-N(6))-methyltransferase Erm(B) | copy | ||
| PGAG | replication/maintenance protein RepL | copy | ||
| PGAG | methyltransferase domain-containing protein | copy | ||
| MOB-typer | rep_cluster_1947 | copy | ||
| Source | Element Name | Display | Sequence | Favorite |
Showing 1 to 6 of 6 entries
Annotations
based on the NCBI Prokaryotic Genome Annotation Pipeline (PGAP)
| NUCCORE ACC | Gene | Locus Tag | Product | Protein id | Codon Start | Translation Table | GO process |
|---|---|---|---|---|---|---|---|
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| NUCCORE ACC | Gene | Locus Tag | Product | Protein id | Codon Start | Translation Table | GO process |
Antimicrobial Resistance
based on NCBIAMRFinder and CARD
| NUCCORE ACC | Analysis Software Name | Reference Database Version | Gene Symbol | Gene Name | Drug Class | Antimicrobial Agent | Gene Start | Gene Stop | Gene Length | Strand Orientation | Sequence Identity (%) | Coverage (%) |
|---|---|---|---|---|---|---|---|---|---|---|---|---|
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| NUCCORE ACC | Analysis Software Name | Reference Database Version | Gene Symbol | Gene Name | Drug Class | Antimicrobial Agent | Gene Start | Gene Stop | Gene Length | Strand Orientation | Sequence Identity (%) | Coverage (%) |
Typing
based on MOB-Typer and Plasmid Multilocus Sequencing Typing (PMLST)
| NUCCORE ACC | Replicon Type | Relaxase Type | MPF Type | OriT Type | Predicted Mobility | Primary Cluster ID | Secondary Cluster ID | Observed Host Range Ncbi Name | Mash Neighbor Distance | Reported Host Range Lit Rank |
|---|---|---|---|---|---|---|---|---|---|---|
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| NUCCORE ACC | Replicon Type | Relaxase Type | MPF Type | OriT Type | Predicted Mobility | Primary Cluster ID | Secondary Cluster ID | Observed Host Range Ncbi Name | Mash Neighbor Distance | Reported Host Range Lit Rank |
BLAST results of detected typing markers by MOB-type
| biomarker | MOB-suite ID | Element | Start | End | Strand | Identity | Coverage | Evalue | Bitscore |
|---|---|---|---|---|---|---|---|---|---|
| replicon | NC001390 | rep_cluster_1947 | 809 | 1295 | plus | 99.591 | 100 | 0 | 891 |
| biomarker | MOB-suite ID | Element | Start | End | Strand | Identity | Coverage | Evalue | Bitscore |
Showing 1 to 1 of 1 entry
Detected typing markers by plasmidfinder
| NUCCORE ACC | Typing | Identity | Coverage | Start | End | Strand | Organism L1 | Organism L2 |
|---|---|---|---|---|---|---|---|---|
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| NUCCORE ACC | Typing | Identity | Coverage | Start | End | Strand | Organism L1 | Organism L2 |