Plasmid NZ_CP050772.1

Sequence

Nucleotide Information

Accession NZ_CP050772.1
Description Salmonella enterica subsp. enterica serovar Indiana strain SI102 plasmid pSI102-1, complete sequence
Source refseq
Topology circular
Length 199036 bp
GC Content 0.47 %
Created at NCBI April 8, 2020



Assembly

Genome Data Information

Accession GCF_012052605.1
Assembly Coverage 202


Biosample

Curated Collection Information
Accession 14450154

PLASMID INFORMATION

GEOGRAPHICAL INFORMATION
Original Query 31.23N;121.47E
Original Query Type coordinates
Coordinates (Lat/Lon) 31.23/121.47
Address People's Square, 120, People's Avenue, Jiangyin, Nanjingdonglu Subdistrict, Shanghai, Huangpu District, Shanghai, 200001, China

ECOSYSTEM
Original Query Homo sapiens,Diarrheal patient
Classification disease,fecal,gastrointestinal_system,host_associated
Host-associated Taxon
  • Homo sapiens (9606)

DISEASE
Original Query None
DOID/SYMP
  • Diarrhea (DOID:13250 )
    • A gastrointestinal system disease described as the condition of having frequent loose or liquid bowel movements. Acute diarrhea is a common cause of death in developing countries and the second most common cause of infant deaths worldwide. The loss of fluids through diarrhea can cause severe dehydration which is one cause of death in diarrhea sufferers. Along with water, sufferers also lose dangerous amounts of important salts, electrolytes, and other nutrients. There are at least four types of diarrhea: secretory diarrhea, osmotic diarrhea, motility-related diarrhea, and inflammatory diarrhea.

Visualization

PNG JSON

Plasmids from same Biosample




Plasmid Visualization

JSON GENBANK

SourceElement Name Display Sequence Favorite
amrfinderplusaac(3)-IVacopy
amrfinderplusaac(6')-Ib-cr5copy
amrfinderplusaph(4)-Iacopy
amrfinderplusaph(3'')-Ibcopy
amrfinderplusfloRcopy
amrfinderplusblaTEMcopy
amrfinderplusblaOXA-1copy
amrfinderpluscatB3copy
rgiBrucella suis mprFcopy
rgiAAC(6')-Ib-cr6copy
SourceElement NameDisplaySequenceFavorite
Showing 1 to 10 of 218 entries
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Annotations

based on the NCBI Prokaryotic Genome Annotation Pipeline (PGAP)
NUCCORE ACCGeneLocus TagProductProtein idCodon StartTranslation TableGO process
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NUCCORE ACCGeneLocus TagProductProtein idCodon StartTranslation TableGO process



Antimicrobial Resistance

based on NCBIAMRFinder and CARD
NUCCORE ACCAnalysis Software NameReference Database VersionGene SymbolGene NameDrug ClassAntimicrobial AgentGene StartGene StopGene LengthStrand OrientationSequence Identity (%)Coverage (%)
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NUCCORE ACCAnalysis Software NameReference Database VersionGene SymbolGene NameDrug ClassAntimicrobial AgentGene StartGene StopGene LengthStrand OrientationSequence Identity (%)Coverage (%)



Typing

based on MOB-Typer and Plasmid Multilocus Sequencing Typing (PMLST)
NUCCORE ACCReplicon TypeRelaxase TypeMPF Type OriT Type Predicted Mobility Primary Cluster ID Secondary Cluster ID Observed Host Range Ncbi NameMash Neighbor DistanceReported Host Range Lit Rank
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NUCCORE ACCReplicon TypeRelaxase TypeMPF TypeOriT TypePredicted MobilityPrimary Cluster IDSecondary Cluster IDObserved Host Range Ncbi NameMash Neighbor DistanceReported Host Range Lit Rank




BLAST results of detected typing markers by MOB-type
biomarkerMOB-suite IDElementStartEndStrandIdentityCoverageEvalueBitscore
mate-pair-formationNC_005211_00005MPF_F27583543plus1001002.33e-172533
mate-pair-formationNC_009838_00006MPF_F35464814plus1001000803
mate-pair-formationNC_005211_00012MPF_T895511633plus10010001873
mate-pair-formationNC_021845_00017MPF_F2955531063plus99.0061000990
mate-pair-formationNC_005211_00030MPF_F3120532260plus99.716990734
repliconBX664015IncHI2A211840plus99.52410001147
replicon000340__KU353730rep_cluster_10885589956861plus10010001779
replicon000155__CP018649IncN147817148498minus1009501260
biomarkerMOB-suite IDElementStartEndStrandIdentityCoverageEvalueBitscore
Showing 1 to 8 of 8 entries


Detected typing markers by plasmidfinder
NUCCORE ACCTypingIdentityCoverageStartEndStrandOrganism L1Organism L2
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NUCCORE ACCTypingIdentityCoverageStartEndStrandOrganism L1Organism L2