LOCUS       NZ_CP044273             1741 bp    DNA     circular CON 10-NOV-2023
DEFINITION  Enterococcus faecium strain V1836 plasmid pHVH-V1836-9, complete
            sequence.
ACCESSION   NZ_CP044273
VERSION     NZ_CP044273.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN12818007
            Assembly: GCF_008728455.1
KEYWORDS    RefSeq.
SOURCE      Enterococcus faecium
  ORGANISM  Enterococcus faecium
            Bacteria; Bacillota; Bacilli; Lactobacillales; Enterococcaceae;
            Enterococcus.
REFERENCE   1  (bases 1 to 1741)
  AUTHORS   Rubin,I.M.C., Pedersen,M.S., Mollerup,S., Kaya,H., Petersen,A.M.,
            Westh,H. and Pinholt,M.
  TITLE     The association between vancomycin-resistant Enterococcus faecium
            colonization and infection: A retrospective WGS study
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 1741)
  AUTHORS   Rubin,I.M.C., Pedersen,M.S., Mollerup,S., Kaya,H., Petersen,A.M.,
            Westh,H. and Pinholt,M.
  TITLE     Direct Submission
  JOURNAL   Submitted (23-SEP-2019) Department of Clinical Microbiology,
            Copenhagen University Hospital Hvidovre, Kettegaard alle 30,
            Hvidovre, Copenhagen 2650, Denmark
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Date                     :: JUL-2019
            Assembly Method                   :: Unicycler v. Version 0.4.7
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 20.0x
            Sequencing Technology :: Illumina MiSeq; Oxford Nanopore MinION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 11/10/2023 05:23:15
            Annotation Pipeline :: NCBI Prokaryotic Genome Annotation Pipeline
            (PGAP)
            Annotation Method :: Best-placed reference protein set; GeneMarkS-2+
            Annotation Software revision      :: 6.6
            Features Annotated                :: Gene; CDS; rRNA; tRNA; ncRNA
            Genes (total)                     :: 3,287
            CDSs (total)                      :: 3,198
            Genes (coding)                    :: 3,028
            CDSs (with protein)               :: 3,028
            Genes (RNA)                       :: 89
            rRNAs                             :: 6, 6, 6 (5S, 16S, 23S)
            complete rRNAs                    :: 6, 6, 6 (5S, 16S, 23S)
            tRNAs                             :: 67
            ncRNAs                            :: 4
            Pseudo Genes (total)              :: 170
            CDSs (without protein)            :: 170
            Pseudo Genes (ambiguous residues) :: 0 of 170
            Pseudo Genes (frameshifted)       :: 82 of 170
            Pseudo Genes (incomplete)         :: 89 of 170
            Pseudo Genes (internal stop)      :: 41 of 170
            Pseudo Genes (multiple problems)  :: 34 of 170
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP044273.1.
            Bacteria and source DNA available from Department of Clinical
            Microbiology, Copenhagen University Hospital Hvidovre, Copenhagen,
            Denmark.
            The annotation was added by the NCBI Prokaryotic Genome Annotation
            Pipeline (PGAP). Information about PGAP can be found here:
            https://www.ncbi.nlm.nih.gov/genome/annotation_prok/
            COMPLETENESS: full length.
FEATURES             Location/Qualifiers
     source          1..1741
                     /organism="Enterococcus faecium"
                     /mol_type="genomic DNA"
                     /strain="V1836"
                     /isolation_source="Rectum"
                     /host="Homo sapiens"
                     /db_xref="taxon:1352"
                     /plasmid="pHVH-V1836-9"
                     /geo_loc_name="Denmark:Copenhagen"
                     /lat_lon="55.67 N 12.56 E"
                     /collection_date="2017"
                     /collected_by="Copenhagen University Hospital Hvidovre"
     gene            complement(join(<1674..1741,1..1297))
                     /gene="aph(2'')-I"
                     /locus_tag="F6439_RS17170"
                     /old_locus_tag="F6439_16685"
                     /pseudo=""
     CDS             complement(join(<1674..1741,1..1297))
                     /gene="aph(2'')-I"
                     /locus_tag="F6439_RS17170"
                     /old_locus_tag="F6439_16685"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_012655884.1"
                     /GO_function="GO:0008080 - N-acetyltransferase activity
                     [Evidence IEA]"
                     /note="incomplete; partial in the middle of a contig;
                     missing C-terminus; Derived by automated computational
                     analysis using gene prediction method: Protein Homology."
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="APH(2'')-Ia/If/Ih family aminoglycoside
                     O-phosphotransferase"
                     /name="aph(2'')-I"
     gene            complement(1298..1690)
                     /locus_tag="F6439_RS16690"
                     /old_locus_tag="F6439_16690"
     CDS             complement(1298..1690)
                     /locus_tag="F6439_RS16690"
                     /old_locus_tag="F6439_16690"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000393259.1"
                     /GO_function="GO:0008080 - N-acetyltransferase activity
                     [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="GNAT family N-acetyltransferase"
                     /protein_id="WP_025189010.1"
                     /translation="MKLLFIDDNMVFDIDNLKGFLNDTSSFGFIAKENNKIIGFAYCYT
                     LLRPDGKTMFYLHSIGMLPNYQDKGYGSKLLSFIKEYSKEIGCSEMFLITDKGNPRACH
                     VYEKLGGKNDYKDEIVYVYDYEKGDK"
                     /name="GNAT family N-acetyltransferase"
     ARG             complement(3..1297)
                     /name="aac(6')-Ie/aph(2'')-Ia"
                     /gene="aac(6')-Ie/aph(2'')-Ia"
                     /gene_name="bifunctional aminoglycoside N-acetyltransferase
                     AAC(6')-Ie/aminoglycoside O-phosphotransferase APH(2'')-Ia"
                     /tool="amrfinderplus"
                     /drug_class="AMINOGLYCOSIDE"
                     /identity="100.0"
                     /coverage="90.19"
     ARG             complement(1672..1739)
                     /name="AAC(6')-Ie-APH(2'')-Ia bifunctional protein"
                     /gene="AAC(6')-Ie-APH(2'')-Ia bifunctional protein"
                     /gene_name="aminoglycoside bifunctional resistance protein"
                     /tool="rgi"
                     /drug_class="aminoglycoside antibiotic"
                     /identity="100.0"
                     /coverage="4.59"
     ARG             complement(3..1297)
                     /name="AAC(6')-Ie-APH(2'')-Ia bifunctional protein"
                     /gene="AAC(6')-Ie-APH(2'')-Ia bifunctional protein"
                     /gene_name="aminoglycoside bifunctional resistance protein"
                     /tool="rgi"
                     /drug_class="aminoglycoside antibiotic"
                     /identity="100.0"
                     /coverage="90.19"
ORIGIN
        1 ctatatttcc atacattctt aatatatctt ctccaaaatt tgttcctatt tcttcttcac
       61 tatcttcaag taagtatata aaatcacaat attcatctat aattccagaa tctccaaaat
      121 caattattcc agttaatcta ttattgccat ctaacaatag atgattacaa ctaaaatcat
      181 tatggcataa acacttttta ccctcaaaaa ctgttgttgc atttagtctt tccataaaac
      241 tttctatata atctttttct atatcagtta aatcattata aatagtttca cgcaacaata
      301 tatactcttc taatacattt tgtttattat caatagtaca ttcactaata tctgtataat
      361 ctaaaccgtg catttgtctt aaaaaactgg caatatctcg ttttaacaaa ttttgttctt
      421 cttctgacat agtagaataa atttctggtg ttaaaaaagt tcctttaatt tctttataac
      481 ctagtataga taattcatca ctaatatacg aatattcaat attaggaatt tttacattag
      541 tttctaaatt tgtatttaaa aaattatata ttgctttttc ttttgcataa ccttttttct
      601 tattagtact aaattttgtt ttaaaaatgt attcattatt aactaaatat gccacactat
      661 cataaccact accgattatt tcaatactat ctactttgaa attatcaaag taatgctcaa
      721 ttaaatattt cattgcctta acatttgtgg cattatcatc atatctatat tccattaaat
      781 aacaatcttc ttttttgccc tcgtgtaatt catgttctgg caaatcttca ataattctaa
      841 aaccagattt ttggtatgcc cttattgctc ttggattatt tttatgaggg tctaaaataa
      901 ctgcattagc atttctttct tttttcaaaa attcaaaaat caatttaata tatcttgtac
      961 caattccttt actccaataa tttggctctc ctataaattg atccatacca tagactatct
     1021 catcagtttt tggataatga taatcagtat ataactcatc atacatttta tatatttgtc
     1081 catatccaat aggaacattg ttatattcaa taattactct aaaaacttca tcttcccaag
     1141 gctctgtata atgttttttt aatgattcta atgtatattt tttatctcta ccaccataaa
     1201 attctaatac tctttcatca gttaaccatt ttaacatcaa aggaaaatca tcatctatta
     1261 aagttcttat acatatttca ttttcaacta tattcattta tttatcacct ttttcataat
     1321 catatacata tactatttca tctttataat catttttacc acctaatttt tcatatacat
     1381 ggcaagctct aggattacct ttatcagtta ttaaaaacat ttcagaacaa ccaatctctt
     1441 tagaatattc cttaataaaa gataataatt ttgaaccata acctttgtct tgatagttag
     1501 gtaacattcc tattgagtgt aaataaaaca ttgtttttcc atcaggtctt aaaagtgtat
     1561 agcaatatgc aaatcctata attttattat tttctttagc tataaaccca aatgaactgg
     1621 tatcattaag aaatcctttt aaattatcaa tatcaaaaac catattatca tcaataaaca
     1681 atagtttcaa taggataata ttcttcaact atatcttgat attcttttgc tttctcaata
     1741 t
//
