Plasmid NZ_CP117361.1
Sequence
Nucleotide Information
| Accession | NZ_CP117361.1 |
|---|---|
| Description | Salmonella enterica subsp. enterica serovar Dublin strain RM094 plasmid pRM094_2, complete sequence |
| Source | refseq |
| Topology | circular |
| Length | 74851 bp |
| GC Content | 0.49 % |
| Created at NCBI | March 3, 2023 |
Host Taxonomy
According to NCBI Taxonomy
| Assigned Host | Salmonella enterica (98360) |
|---|
Lineage
| Superkingdom | Bacteria (2) |
|---|---|
| Phylum | Pseudomonadota (1224) |
| Class | Gammaproteobacteria (1236) |
| Order | Enterobacterales (91347) |
| Family | Enterobacteriaceae (543) |
| Genus | Salmonella (590) |
| Species | Salmonella_enterica (28901) |
| Strain |
Biosample
Curated Collection Information
| Accession | 32950792 |
|---|
PLASMID INFORMATION
GEOGRAPHICAL INFORMATION
| Original Query | USA,Nebraska |
|---|---|
| Original Query Type | name |
| Coordinates (Lat/Lon) | 41.74/-99.59 |
| Address | USA,Nebraska |
ECOSYSTEM
| Original Query | Bos taurus,Liver, lung, small intestine |
|---|---|
| Classification | gastrointestinal_system,host_associated,liver,lung,respiratory_system,small_gut |
| Host-associated Taxon |
|
DISEASE
| Original Query | Pneumonia, septicemia |
|---|---|
| DOID/SYMP |
|
Visualization
Plasmids from same Biosample
Similar Plasmids
based on Mash distance
Plasmid Visualization
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| Source | Element Name | Display | Sequence | Favorite |
|---|---|---|---|---|
| amrfinderplus | spvD | copy | ||
| PGAG | repA | copy | ||
| PGAG | transposase | copy | ||
| PGAG | hypothetical protein | copy | ||
| PGAG | hypothetical protein | copy | ||
| PGAG | hypothetical protein | copy | ||
| PGAG | faeH | copy | ||
| PGAG | K88 minor fimbrial subunit faeI | copy | ||
| PGAG | hypothetical protein | copy | ||
| PGAG | hypothetical protein | copy | ||
| Source | Element Name | Display | Sequence | Favorite |
Showing 1 to 10 of 92 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 |
|---|---|---|---|---|---|---|---|---|---|
| mate-pair-formation | NC_023277_00163 | MPF_T | 48396 | 50546 | plus | 99.861 | 100 | 0 | 1457 |
| mate-pair-formation | NC_013503_00034 | MPF_T | 51556 | 52686 | plus | 98.939 | 100 | 0 | 652 |
| mate-pair-formation | NC_019067_00043 | MPF_T | 52934 | 53644 | plus | 99.578 | 100 | 4.87e-137 | 431 |
| mate-pair-formation | NC_010860_00022 | MPF_T | 53652 | 54578 | plus | 98.058 | 100 | 0 | 625 |
| mate-pair-formation | NC_017624_00009 | MPF_T | 56818 | 58614 | plus | 98.831 | 98 | 0 | 1186 |
| replicon | 000114__CP015527 | IncFII | 1 | 882 | plus | 98.753 | 100 | 0 | 1568 |
| replicon | 000217__NC_019106_00041 | IncX1 | 38570 | 39016 | minus | 100 | 100 | 0 | 826 |
| replicon | LS992172_00069 | IncFII | 74587 | 74851 | minus | 83.704 | 86 | 4.96e-61 | 241 |
| relaxase | NC_019096_00001 | MOBP | 44636 | 45799 | plus | 98.454 | 100 | 0 | 790 |
| relaxase | CP030220_00041 | MOBF | 67280 | 71542 | plus | 88.202 | 81 | 0 | 2463 |
| biomarker | MOB-suite ID | Element | Start | End | Strand | Identity | Coverage | Evalue | Bitscore |
Showing 1 to 10 of 10 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 |