Plasmid NZ_CP140626.1
Sequence
Nucleotide Information
| Accession | NZ_CP140626.1 |
|---|---|
| Description | Shigella sonnei strain ST152 plasmid pSO87_sm008, complete sequence |
| Source | refseq |
| Topology | circular |
| Length | 5631 bp |
| GC Content | 0.47 % |
| Created at NCBI | Jan. 7, 2024 |
Host Taxonomy
According to NCBI Taxonomy
| Assigned Host | Shigella sonnei (624) |
|---|
Lineage
| Superkingdom | Bacteria (2) |
|---|---|
| Phylum | Pseudomonadota (1224) |
| Class | Gammaproteobacteria (1236) |
| Order | Enterobacterales (91347) |
| Family | Enterobacteriaceae (543) |
| Genus | Shigella (620) |
| Species | Shigella_sonnei (624) |
| Strain |
Biosample
Curated Collection Information
| Accession | 32329321 |
|---|
PLASMID INFORMATION
GEOGRAPHICAL INFORMATION
| Original Query | 44.4912N;11.3615E |
|---|---|
| Original Query Type | coordinates |
| Coordinates (Lat/Lon) | 44.49/11.36 |
| Address | Accesso Ematologia, Cirenaica, San Donato-San Vitale, Bologna, Emilia-Romagna, 40125, Italy |
ECOSYSTEM
| Original Query | Homo sapiens,stool |
|---|---|
| Classification | fecal,gastrointestinal_system,host_associated |
| Host-associated Taxon |
|
| Host-associated Sex | male |
DISEASE
| Original Query | Shigellosis |
|---|---|
| DOID/SYMP |
|
Visualization
Similar Plasmids
based on Mash distance
Plasmid Visualization
Grays
Blues
Purples
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Oranges
Greens
100
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R
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B
| Source | Element Name | Display | Sequence | Favorite |
|---|---|---|---|---|
| PGAG | hypothetical protein | copy | ||
| PGAG | DMT family transporter | copy | ||
| PGAG | Rop family plasmid primer RNA-binding protein | copy | ||
| PGAG | MobC family plasmid mobilization relaxosome protein | copy | ||
| PGAG | MbeB family mobilization protein | copy | ||
| PGAG | MbeD family mobilization/exclusion protein | copy | ||
| MOB-typer | MOBP | copy | ||
| MOB-typer | MOBP | copy | ||
| MOB-typer | rep_cluster_2401 | copy | ||
| Source | Element Name | Display | Sequence | Favorite |
Showing 1 to 9 of 9 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 |
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 | CP039864_00003 | rep_cluster_2401 | 1769 | 1957 | plus | 100 | 100 | 4.63e-94 | 350 |
| relaxase | NC_022662_00003 | MOBP | 3158 | 4720 | plus | 100 | 100 | 0 | 1004 |
| oriT | NC_019078 | MOBP | 2413 | 2495 | plus | 100 | 100 | 1.3400000000000002e-35 | 154 |
| biomarker | MOB-suite ID | Element | Start | End | Strand | Identity | Coverage | Evalue | Bitscore |
Showing 1 to 3 of 3 entries
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 |