Plasmid NZ_CP039299.1

Sequence

Nucleotide Information

Accession NZ_CP039299.1
Description Escherichia coli strain PigCaeca_1 plasmid unnamed1, complete sequence
Source refseq
Topology circular
Length 105771 bp
GC Content 0.49 %
Created at NCBI April 24, 2019



Assembly

Genome Data Information

Accession GCF_004801575.1
Assembly Coverage 30


Biosample

Curated Collection Information
Accession 11268909

PLASMID INFORMATION

GEOGRAPHICAL INFORMATION
Original Query 53.91N;1.03W
Original Query Type coordinates
Coordinates (Lat/Lon) 53.91/-1.03
Address Wheldrake Lane, Deighton, York, England, YO19 4SQ, United Kingdom

ECOSYSTEM
Original Query pig,Single colony culture,feces
Classification cell_culture,fecal,gastrointestinal_system,host_associated
Host-associated Taxon

DISEASE
Original Query None
DOID/SYMP

Visualization

PNG JSON

Plasmids from same Biosample



Similar Plasmids

based on Mash distance

NZ_CP039299.1 See Comparison


Plasmid Visualization

JSON GENBANK

SourceElement Name Display Sequence Favorite
amrfinderplusqnrS1copy
PGAGrepAcopy
PGAGhypothetical proteincopy
PGAGyacAcopy
PGAGyacBcopy
PGAGhypothetical proteincopy
PGAGhypothetical proteincopy
PGAGAbi family proteincopy
PGAGplasmid pRiA4b ORF-3 family proteincopy
PGAGrecombinase family proteincopy
SourceElement NameDisplaySequenceFavorite
Showing 1 to 10 of 127 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_019097_00056MPF_I5246554726minus98.8069201446
mate-pair-formationNC_022267_00057MPF_I6633667535minus97.251000751
mate-pair-formationNC_019111_00038MPF_I7231372690minus100942.5999999999999997e-47169
mate-pair-formationNC_023290_00086MPF_I7274473268minus99.4291003.4400000000000003e-100322
mate-pair-formationNC_015965_00072MPF_I7327173972minus99.5731004.56e-153477
mate-pair-formationNC_019097_00075MPF_I7526776247minus1001000658
mate-pair-formationNC_022267_00069MPF_I7630376950minus99.074915.71e-143448
mate-pair-formationNZ_CM001473_00069MPF_I7695077294minus91.3791001.6799999999999995e-54189
mate-pair-formationNC_019097_00085MPF_I8317083985minus1001004.32e-178550
oriTHM021326MOBP4825748349minus1001004.37e-41172
biomarkerMOB-suite IDElementStartEndStrandIdentityCoverageEvalueBitscore
Showing 1 to 10 of 12 entries


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