Plasmid NZ_CP014968.1
Sequence
Nucleotide Information
| Accession | NZ_CP014968.1 |
|---|---|
| Description | Salmonella enterica subsp. enterica serovar Typhimurium str. CDC 2011K-1702 isolate USDA-ARS-USMARC-1910 plasmid pSTY1-2011K-1702, complete sequence |
| Source | refseq |
| Topology | circular |
| Length | 94016 bp |
| GC Content | 0.53 % |
| Created at NCBI | April 21, 2016 |
Host Taxonomy
According to NCBI Taxonomy
Lineage
| Superkingdom | Bacteria (2) |
|---|---|
| Phylum | Pseudomonadota (1224) |
| Class | Gammaproteobacteria (1236) |
| Order | Enterobacterales (91347) |
| Family | Enterobacteriaceae (543) |
| Genus | Salmonella (590) |
| Species | Salmonella_enterica (28901) |
| Strain | Salmonella_enterica_subsp._enterica_serovar_Typhimurium_str._CDC_2011K-1702 (1454643) |
Biosample
Curated Collection Information
| Accession | 2716880 |
|---|
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 | None |
|---|---|
| DOID/SYMP |
Visualization
Similar Plasmids
based on Mash distance
Plasmid Visualization
Grays
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100
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B
| Source | Element Name | Display | Sequence | Favorite |
|---|---|---|---|---|
| amrfinderplus | spvD | copy | ||
| PGAG | hypothetical protein | copy | ||
| PGAG | hypothetical protein | copy | ||
| PGAG | replication regulatory protein RepA | copy | ||
| PGAG | tap | copy | ||
| PGAG | repA | copy | ||
| PGAG | SdiA-regulated domain-containing protein | copy | ||
| PGAG | AraC family transcriptional regulator | copy | ||
| PGAG | rck | copy | ||
| PGAG | YjiK family protein | copy | ||
| Source | Element Name | Display | Sequence | Favorite |
Showing 1 to 10 of 121 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 | 000114__CP015527 | IncFII | 1908 | 2789 | plus | 99.546 | 100 | 0 | 1607 |
| replicon | 000101__NZ_CP012345_00042 | IncFIB | 16636 | 17707 | minus | 93.097 | 100 | 0 | 1568 |
| relaxase | NC_007208_00043 | MOBF | 87360 | 92516 | plus | 95.637 | 98 | 0 | 3248 |
| mate-pair-formation | NC_022651_00077 | MPF_F | 63073 | 63381 | plus | 92.233 | 99 | 2.21e-59 | 202 |
| mate-pair-formation | NC_019002_00072 | MPF_F | 63959 | 64696 | plus | 97.561 | 100 | 1.38e-147 | 462 |
| mate-pair-formation | NC_019094_00090 | MPF_F | 64699 | 66087 | plus | 90.773 | 96 | 0 | 796 |
| mate-pair-formation | NC_019112_00063 | MPF_F | 66926 | 67438 | plus | 91.813 | 100 | 3.2799999999999998e-90 | 293 |
| mate-pair-formation | NC_013437_00116 | MPF_T | 68653 | 71298 | plus | 99.773 | 100 | 0 | 1797 |
| mate-pair-formation | NC_017054_00095 | MPF_F | 71659 | 72288 | plus | 99.524 | 100 | 1.34e-136 | 428 |
| mate-pair-formation | NC_017054_00096 | MPF_F | 72288 | 73277 | plus | 100 | 100 | 0 | 664 |
| biomarker | MOB-suite ID | Element | Start | End | Strand | Identity | Coverage | Evalue | Bitscore |
Showing 1 to 10 of 14 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 |