Plasmid NZ_CP092543.1
Sequence
Nucleotide Information
| Accession | NZ_CP092543.1 |
|---|---|
| Description | Staphylococcus aureus strain VRMSSA-WC113 plasmid unnamed, complete sequence |
| Source | refseq |
| Topology | circular |
| Length | 24653 bp |
| GC Content | 0.29 % |
| Created at NCBI | March 26, 2022 |
Host Taxonomy
According to NCBI Taxonomy
| Assigned Host | Staphylococcus aureus (1280) |
|---|
Lineage
| Superkingdom | Bacteria (2) |
|---|---|
| Phylum | Bacillota (1239) |
| Class | Bacilli (91061) |
| Order | Bacillales (1385) |
| Family | Staphylococcaceae (90964) |
| Genus | Staphylococcus (1279) |
| Species | Staphylococcus_aureus (1280) |
| Strain |
Biosample
Curated Collection Information
| Accession | 26026640 |
|---|
PLASMID INFORMATION
GEOGRAPHICAL INFORMATION
| Original Query | USA |
|---|---|
| Original Query Type | name |
| Coordinates (Lat/Lon) | 39.78/-100.45 |
| Address | USA |
ECOSYSTEM
| Original Query | Homo sapiens,urine |
|---|---|
| Classification | host_associated,urinary_system |
| Host-associated Taxon |
|
DISEASE
| Original Query | UTI |
|---|---|
| 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 | PC1 beta-lactamase (blaZ) | copy | ||
| amrfinderplus | arsB | copy | ||
| amrfinderplus | arsC | copy | ||
| amrfinderplus | blaI | copy | ||
| amrfinderplus | cadD | copy | ||
| amrfinderplus | arsR | copy | ||
| amrfinderplus | blaR1 | copy | ||
| amrfinderplus | blaZ | copy | ||
| PGAG | replication initiator protein A | copy | ||
| PGAG | hypothetical protein | copy | ||
| Source | Element Name | Display | Sequence | Favorite |
Showing 1 to 10 of 36 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 |
|---|---|---|---|---|---|---|---|
| Loading... | |||||||
| 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 (%) |
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| AB011549.2 | amrfinderplus | 2024-01-31.1 | toxB | toxin B | 55981 | 65487 | -1 | + | 100.0 | 100.0 | ||
| AB011549.2 | amrfinderplus | 2024-01-31.1 | espP | serine protease autotransporter EspP | 80757 | 84656 | -1 | + | 100.0 | 100.0 | ||
| AB011549.2 | amrfinderplus | 2024-01-31.1 | katP | catalase/peroxidase KatP | 76888 | 79095 | -1 | + | 100.0 | 100.0 | ||
| AB011549.2 | amrfinderplus | 2024-01-31.1 | ehxA | enterohemolysin EhxA | 16612 | 19605 | -1 | + | 100.0 | 100.0 | ||
| AB576781.2 | amrfinderplus | 2024-01-31.1 | blaTEM-1 | broad-spectrum class A beta-lactamase TEM-1 | BETA-LACTAM | BETA-LACTAM | 28587 | 29444 | -1 | - | 100.0 | 100.0 |
| AB576781.2 | amrfinderplus | 2024-01-31.1 | qacEdelta1 | quaternary ammonium compound efflux SMR transporter QacE delta 1 | QUATERNARY AMMONIUM | QUATERNARY AMMONIUM | 16844 | 17188 | -1 | - | 100.0 | 100.0 |
| AB576781.2 | amrfinderplus | 2024-01-31.1 | tet(A) | tetracycline efflux MFS transporter Tet(A) | TETRACYCLINE | TETRACYCLINE | 9712 | 10908 | -1 | - | 100.0 | 100.0 |
| AB576781.2 | amrfinderplus | 2024-01-31.1 | sul1 | sulfonamide-resistant dihydropteroate synthase Sul1 | SULFONAMIDE | SULFONAMIDE | 16011 | 16847 | -1 | - | 100.0 | 100.0 |
| AB576781.2 | amrfinderplus | 2024-01-31.1 | aph(3')-Ia | aminoglycoside O-phosphotransferase APH(3')-Ia | AMINOGLYCOSIDE | KANAMYCIN | 5065 | 5877 | -1 | + | 100.0 | 100.0 |
| AB576781.2 | amrfinderplus | 2024-01-31.1 | spvD | SPI-2 type III secretion system effector cysteine hydrolase SpvD | 42154 | 42801 | -1 | - | 100.0 | 100.0 | ||
| 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 (%) |
Showing 1 to 10 of 250,691 entries (filtered from 251,138 total entries)
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Biosynthetic Gene Clusters
based on ANTISMASH
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 |
|---|---|---|---|---|---|---|---|---|---|---|
| AB000510.1 | non-mobilizable | AD045 | AM462 | Candidatus Phytoplasma | 0.0 | |||||
| AB011548.2 | rep_cluster_2350 | MOBF | MOB_unknown | mobilizable | AA667 | AI941 | Actinomycetota,Bacillota,Bacteroidota,Pseudomonadota | 0.0 | genus | |
| AB011549.2 | IncFIA,IncFIB | non-mobilizable | AA345 | AI296 | Enterobacterales | 0.0 | order | |||
| AB063523.1 | rep_cluster_1526 | non-mobilizable | AE201 | AN929 | Wigglesworthia | 0.0 | ||||
| AB244976.1 | rep_cluster_1617 | MOBP | MPF_T | MOBQ | conjugative | AC441 | AL633 | Sphingomonadaceae | 0.00940624 | |
| AB576781.2 | IncFII | MOBF | MPF_F | conjugative | AB460 | AK247 | Enterobacterales | 0.0 | family | |
| AB605179.1 | IncFIB,IncFII | MOBF | MPF_F | conjugative | AB460 | AK247 | Enterobacterales | 0.0 | order | |
| ADWM02000138.1 | non-mobilizable | AF844 | AP846 | Neisseria | 0.00058191 | |||||
| ADWN02000004.1 | non-mobilizable | AF844 | AP846 | Neisseria | 0.00058191 | |||||
| AE006471.2 | IncFIB,IncFII | MOBF | MPF_F | conjugative | AB460 | AK247 | Enterobacterales | 0.0 | order | |
| 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 |
Showing 1 to 10 of 72,360 entries (filtered from 72,556 total entries)
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BLAST results of detected typing markers by MOB-type
| biomarker | MOB-suite ID | Element | Start | End | Strand | Identity | Coverage | Evalue | Bitscore |
|---|---|---|---|---|---|---|---|---|---|
| oriT | AF001314 | MOBQ | 1349 | 1497 | plus | 100 | 100 | 5.980000000000001e-72 | 276 |
| replicon | AP003139 | rep_cluster_2100 | 1 | 984 | plus | 99.593 | 100 | 0 | 1796 |
| replicon | 000261__GQ900456 | rep_cluster_1017 | 1115 | 1285 | plus | 93.605 | 91 | 1.04e-65 | 255 |
| replicon | AP003139 | rep_cluster_2214 | 21337 | 22197 | plus | 99.768 | 100 | 0 | 1580 |
| replicon | CP000737 | rep_cluster_1733 | 23485 | 24228 | minus | 100 | 100 | 0 | 1375 |
| relaxase | AB304512_00007 | MOBV | 19764 | 20138 | plus | 99.2 | 100 | 1.03e-73 | 244 |
| biomarker | MOB-suite ID | Element | Start | End | Strand | Identity | Coverage | Evalue | Bitscore |
Showing 1 to 6 of 6 entries
Detected typing markers by plasmidfinder
| NUCCORE ACC | Typing | Identity | Coverage | Start | End | Strand | Organism L1 | Organism L2 |
|---|---|---|---|---|---|---|---|---|
| AB011548.2 | ColRNAI | 87.02 | 100.0 | 2675 | 2805 | plus | Enterobacteriales | enterobacteriales |
| AB011549.2 | IncFII | 96.17 | 99.23 | 72300 | 72558 | plus | Enterobacteriales | enterobacteriales |
| AB011549.2 | IncFIB(AP001918) | 98.24 | 100.0 | 25716 | 26397 | plus | Enterobacteriales | enterobacteriales |
| AB576781.2 | IncFII(S) | 100.0 | 100.0 | 111401 | 111662 | plus | Enterobacteriales | enterobacteriales |
| AB576781.2 | IncFII(pAR0022) | 85.29 | 98.42 | 111685 | 112119 | plus | Enterobacteriales | enterobacteriales |
| AB605179.1 | IncFII(S) | 100.0 | 100.0 | 131573 | 131834 | plus | Enterobacteriales | enterobacteriales |
| AB605179.1 | IncFIB(AP001918) | 98.39 | 100.0 | 20534 | 21215 | plus | Enterobacteriales | enterobacteriales |
| AB605179.1 | IncFII(pAR0022) | 85.29 | 98.42 | 131857 | 132291 | plus | Enterobacteriales | enterobacteriales |
| AE006471.2 | IncFIB(S) | 100.0 | 100.0 | 17011 | 17653 | plus | Enterobacteriales | enterobacteriales |
| AE006471.2 | IncFII(S) | 100.0 | 100.0 | 1665 | 1926 | plus | Enterobacteriales | enterobacteriales |
| NUCCORE ACC | Typing | Identity | Coverage | Start | End | Strand | Organism L1 | Organism L2 |
Showing 1 to 10 of 60,619 entries
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