Plasmid NZ_CP082121.1

Sequence

Nucleotide Information

Accession NZ_CP082121.1
Description Escherichia coli strain PC-NDM34 plasmid pIncFIA, complete sequence
Source refseq
Topology circular
Length 109135 bp
GC Content 0.51 %
Created at NCBI Sept. 2, 2021



Assembly

Genome Data Information

Accession GCF_019843995.1
Assembly Coverage 53.2


Biosample

Curated Collection Information
Accession 20857175

PLASMID INFORMATION

GEOGRAPHICAL INFORMATION
Original Query 6.7924S;39.2083E
Original Query Type coordinates
Coordinates (Lat/Lon) -6.79/39.21
Address Morogoro Road, Kibo, Ubungo, Ubungo Municipal, Dar es-Salaam, Coastal Zone, 21493, Tanzania

ECOSYSTEM
Original Query Homo sapiens,rectal swab from HIV infected patient
Classification disease,gastrointestinal_system,host_associated,rectal
Host-associated Taxon
  • Homo sapiens (9606)

DISEASE
Original Query Gut colonization
DOID/SYMP
  • Human immunodeficiency virus infectious disease (DOID:526 )
    • A viral infectious disease that results in destruction of immune system, leading to life-threatening opportunistic infections and cancers, has_material_basis_in Human immunodeficiency virus 1 or has_material_basis_in Human immunodeficiency virus 2, which are transmitted by sexual contact, transmitted by transfer of blood, semen, vaginal fluid, pre-ejaculate, or breast milk, transmitted by congenital method, and transmitted by contaminated needles. The virus infects helper T cells (CD4+ T cells) which are directly or indirectly destroyed, macrophages, and dendritic cells. The infection has symptom diarrhea, has symptom fatigue, has symptom fever, has symptom vaginal yeast infection, has symptom headache, has symptom mouth sores, has symptom muscle aches, has symptom sore throat, and has symptom swollen lymph glands.
    • Has_material_basis_in: ['human immunodeficiency virus 1 or has_material_basis_in human immunodeficiency virus 2']

Visualization

PNG JSON

Plasmids from same Biosample




Plasmid Visualization

JSON GENBANK

NUCCORE ACC Source Element Name Display Sequence Favorite
NUCCORE ACC Source Element Name Display Sequence Favorite



Annotations

based on the NCBI Prokaryotic Genome Annotation Pipeline (PGAP)
NUCCORE ACC Gene Locus Tag Product Protein id Codon Start Translation Table GO process
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 (%)
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 Contigs md5 hash Replicon Type Relaxase Type MPF Type OriT Type Predicted Mobility Primary Cluster ID Secondary Cluster ID Observed Host Range Ncbi Rank Observed Host Range Ncbi Name Mash Nearest Neighbor Mash Neighbor Distance Mash Neighbor Identification Reported Host Range Lit Rank Reported Host Range Lit Name Replicon Type Accession Relaxase Type Accession MPF Type Accession OriT Type Accession Associated PMID(s)
NUCCORE ACC Contigs md5 hash Replicon Type Relaxase Type MPF Type OriT Type Predicted Mobility Primary Cluster ID Secondary Cluster ID Observed Host Range Ncbi Rank Observed Host Range Ncbi Name Mash Nearest Neighbor Mash Neighbor Distance Mash Neighbor Identification Reported Host Range Lit Rank Reported Host Range Lit Name Replicon Type Accession Relaxase Type Accession MPF Type Accession OriT Type Accession Associated PMID(s)




BLAST results of detected typing markers by MOB-type
NUCCORE ACC biomarker MOB-suite ID Element Start End Strand Identity Coverage Evalue Bitscore
NUCCORE ACC biomarker MOB-suite ID Element Start End Strand Identity Coverage Evalue Bitscore