Plasmid NZ_KY471629.1
Sequence
Nucleotide Information
| Accession | NZ_KY471629.1 |
|---|---|
| Description | Shigella sonnei strain SH15sh105 plasmid pSH15sh104, complete sequence |
| Source | refseq |
| Topology | circular |
| Length | 104285 bp |
| GC Content | 0.53 % |
| Created at NCBI | May 18, 2020 |
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 | 14227524 |
|---|
PLASMID INFORMATION
GEOGRAPHICAL INFORMATION
| Original Query | China |
|---|---|
| Original Query Type | name |
| Coordinates (Lat/Lon) | 34.41/86.03 |
| Address | China |
ECOSYSTEM
| Original Query | patient feces |
|---|---|
| Classification | fecal,gastrointestinal_system,host_associated |
| Host-associated Taxon |
|
DISEASE
| Original Query | None |
|---|---|
| DOID/SYMP |
Visualization
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 | mphA | copy | ||
| amrfinderplus | blaCTX-M-14 | copy | ||
| rgi | Mrx | copy | ||
| amrfinderplus | mph(A) | copy | ||
| amrfinderplus | aac(3)-IId | copy | ||
| PGAG | repA | copy | ||
| PGAG | ribbon-helix-helix domain-containing protein | copy | ||
| PGAG | type II toxin-antitoxin system RelE/ParE family toxin | copy | ||
| PGAG | hypothetical protein | copy | ||
| PGAG | hypothetical protein | copy | ||
| Source | Element Name | Display | Sequence | Favorite |
Showing 1 to 10 of 135 entries
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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 | KR905388 | IncK2/Z | 1 | 873 | plus | 98.625 | 100 | 0 | 1546 |
| relaxase | NC_013728_00087 | MOBP | 44056 | 46764 | plus | 90.397 | 100 | 0 | 1629 |
| mate-pair-formation | NC_011754_00087 | MPF_I | 48064 | 50364 | minus | 99.218 | 100 | 0 | 1427 |
| mate-pair-formation | NC_014843_00047 | MPF_I | 62639 | 63841 | minus | 100 | 100 | 0 | 733 |
| mate-pair-formation | NC_007365_00035 | MPF_I | 68802 | 69152 | minus | 89.744 | 89 | 2.25e-51 | 181 |
| mate-pair-formation | NC_011754_00109 | MPF_I | 69247 | 69774 | minus | 99.432 | 100 | 1.56e-100 | 323 |
| mate-pair-formation | NC_014843_00041 | MPF_I | 69774 | 70484 | minus | 97.89 | 100 | 1.08e-152 | 476 |
| mate-pair-formation | NC_022371_00084 | MPF_I | 71825 | 72796 | minus | 99.383 | 100 | 0 | 580 |
| mate-pair-formation | NC_012487_00131 | MPF_I | 72810 | 73502 | minus | 99.567 | 100 | 1.17e-152 | 476 |
| mate-pair-formation | NC_022992_00098 | MPF_I | 73517 | 73864 | minus | 93.103 | 100 | 1.08e-48 | 172 |
| biomarker | MOB-suite ID | Element | Start | End | Strand | Identity | Coverage | Evalue | Bitscore |
Showing 1 to 10 of 12 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 |