LOCUS       NZ_CP044272             4374 bp    DNA     circular CON 10-NOV-2023
DEFINITION  Enterococcus faecium strain V1836 plasmid pHVH-V1836-8, complete
            sequence.
ACCESSION   NZ_CP044272
VERSION     NZ_CP044272.1
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 4374)
  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  JOURNAL   Unpublished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 4374)
  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
            CP044272.1.
            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..4374
                     /organism="Enterococcus faecium"
                     /mol_type="genomic DNA"
                     /strain="V1836"
                     /isolation_source="Rectum"
                     /host="Homo sapiens"
                     /db_xref="taxon:1352"
                     /plasmid="pHVH-V1836-8"
                     /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(3090..4374,1..122))
                     /locus_tag="F6439_RS16655"
                     /old_locus_tag="F6439_16655"
     CDS             complement(join(3090..4374,1..122))
                     /locus_tag="F6439_RS16655"
                     /old_locus_tag="F6439_16655"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_016173818.1"
                     /GO_function="GO:0003677 - DNA binding [Evidence IEA]"
                     /GO_process="GO:0006310 - DNA recombination [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="plasmid recombination protein"
                     /protein_id="WP_060804915.1"
                     /translation="MGFSISFKKGTKNTSISHNNRELTDSQKTNDWHKHIDFTKSDENI
                     YLEQTNLADKYEELFGEVVEKYNAKQKRADRKIEDYLAKVRKDKKLEPQREFIVQIGIL
                     DDFQTNRADGSSTGISKQQAEQNRVIANKILVQYYKEFQERNPNLAVYNAVIHNDEISP
                     HLHLNIVPVAEGYKRGVQKQPSFNKALVQQGIHADKDNGRVLFNNFRNQEVDSIERLMN
                     DYGWKRDIVGTNKIKDIHEYKEIMSEISELRQTAVKERESVSDELRYIYRQREENERDK
                     ALMASERAKIEEEKKNMLNVKKEMAVIFQKDMVPLESFKRLPDGSYHLSGNDFVDLYQR
                     ATRATNAKRNADNMSEQYLQMLEQNTELNEYVATLEEERHLSGRKQLADLQVENKKLKE
                     ENRSLRQRLERLKNAFQKSITRLSIRFGLAEKDMGLSEELEVLEQEKTLFYRQNVSQRK
                     LERSEDEIEW"
                     /name="plasmid recombination protein"
     gene            complement(344..706)
                     /locus_tag="F6439_RS16660"
                     /old_locus_tag="F6439_16660"
     CDS             complement(344..706)
                     /locus_tag="F6439_RS16660"
                     /old_locus_tag="F6439_16660"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_016173819.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_060804916.1"
                     /translation="MGMTLADIKAQEEKLKKEQAKLRQQKKRLIEKENAAMGKALRKRF
                     GFETFADFERWLSSISDDQQHEKSVDNEWLADEKSAPSERDYPNESDGLLGVIPSKKSQ
                     MSESKFTSMFNDVSLR"
                     /name="hypothetical protein"
     gene            complement(710..1048)
                     /locus_tag="F6439_RS16665"
                     /old_locus_tag="F6439_16665"
     CDS             complement(710..1048)
                     /locus_tag="F6439_RS16665"
                     /old_locus_tag="F6439_16665"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_002321903.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_002321903.1"
                     /translation="MVAILEVRCDMDKIDLREETVDRIELMYERLADYLNLPDEDNYSE
                     MLERMMDVLNSVINADLAKSSVLTNEFVHKHLAQTTDESEKEFWLKLMSHVMQLNQISV
                     INSKEKEM"
                     /name="hypothetical protein"
     gene            complement(1027..1446)
                     /locus_tag="F6439_RS16670"
                     /old_locus_tag="F6439_16670"
     CDS             complement(1027..1446)
                     /locus_tag="F6439_RS16670"
                     /old_locus_tag="F6439_16670"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_002351943.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_002298420.1"
                     /translation="MTDLPEKMTIKNLADELGISKNTVRNQLVNAGYDLARYKDNGVIM
                     LDKELIGVVRSIYRSKGGQLTGDLPVNDAGNDFPLEKENEFLREQLAEKDRHISELTEM
                     IRDQQKLTLLQQQKNDQLLLENQELKNRKWWQFWK"
                     /name="hypothetical protein"
     gene            complement(1439..1672)
                     /locus_tag="F6439_RS16675"
                     /old_locus_tag="F6439_16675"
     CDS             complement(1439..1672)
                     /locus_tag="F6439_RS16675"
                     /old_locus_tag="F6439_16675"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_002298421.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_002298421.1"
                     /translation="MAEKQKHFGKKNWLVNLTGDNVVVVFLDSKKMSGKLLDVTQYELI
                     LKNNKIDSPIIIPKHAVKYVYGVAESNGEDND"
                     /name="hypothetical protein"
     gene            complement(1675..2643)
                     /locus_tag="F6439_RS16680"
                     /old_locus_tag="F6439_16680"
     CDS             complement(1675..2643)
                     /locus_tag="F6439_RS16680"
                     /old_locus_tag="F6439_16680"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_002298422.1"
                     /GO_function="GO:0003677 - DNA binding [Evidence IEA];
                     GO:0003916 - DNA topoisomerase activity [Evidence IEA]"
                     /GO_process="GO:0006270 - DNA replication initiation
                     [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="replication initiation factor domain-containing
                     protein"
                     /protein_id="WP_151076514.1"
                     /translation="MSKNGIIVNEWENLTALSNRRLNVQNLNTPLKLQWSIDRITIVGK
                     LKENIYYHTQNDVLILDFEQLMRVNEGNGYLKAVGNNGWQLLDQYEENIAYIEILKWQD
                     GKGRIDFNPNKIGHFLASSMKNFIHDLFLEPHFSRADIACDIIDVPDEFITQYRVVDPV
                     SFKPIYGRSGKLETAYWGSRASERQIRLYNKKLEQETKRKIVPPEIETWWRLELQLRRG
                     KATDWHAMVHESLNSFASPHFLPLDVKTNDKVMIFGLIANPEMWGFLERRMKYKLRDIL
                     KRESQNDELTNHLRETFSESADVLKKELDTWLQGLDVTEEE"
                     /name="replication initiation factor domain-containing
                     protein"
     Typing          complement(1683..2565)
                     /name="rep_cluster_943"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="84.287"
                     /coverage="98.0"
                     /evalue="0.0"
     Typing          complement(3094..4373)
                     /name="MOBV"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="92.037"
                     /coverage="99.0"
                     /evalue="0.0"
ORIGIN
        1 gatttcgtga agtcaatatg cttatgccaa tcattggttt tctggctatc agttaactca
       61 cgattattat gagaaatact tgtattcttc gttccttttt taaatgaaat actaaacccc
      121 aagttaaaac cctccttcgc gctgtcgcta ataaaaagag tgtaaacctt tctgttactc
      181 tttgtcaaag agtaacattt tcctaattgt gacatggctg tcacaattcc aaatgctctc
      241 cgagggtatt cgctgtcaca agtgacaacg aaaaaaggag ccgaaagcgt gtcacgctct
      301 caactccttt tacgctttat tttgcttcac gcaaaataat cgcttatcgt aaactcacgt
      361 cattaaacat tgacgtaaat ttactctcac tcatctgact ttttttactc ggtatcactc
      421 cgagtaagcc gtcagattca ttgggataat ctcgttcgct tggcgctgat ttttcatcag
      481 caagccactc attatccact gatttttcgt gttgctgatc gtcagaaatc gacgatagcc
      541 accgctcaaa atcagcaaaa gtttcaaacc caaaacgctt gcgaagagcc ttgcccattg
      601 cagcattttc tttctcaatc aagcgttttt tctgttggcg aagtttcgct tgttcttttt
      661 ttaatttttc ttcttgcgct ttaatatctg ctaaagtcat tcccataaac tacatctcct
      721 tttctttgga attaataacg gaaatttggt ttaactgcat aacatgactc attaatttca
      781 accaaaattc tttttctgat tcatcagttg tttgcgctaa atgcttatga acaaattcat
      841 tagtcaaaac tgaagatttt gctagatcag cattgataac cgagttgaga acatccatca
      901 ttcgttcaag catttcacta taattatctt catccggcaa attcaaataa tcagctaacc
      961 gttcatacat caattcaatt ctatcgactg tttcttctct caaatcaatt ttatccatgt
     1021 cacacctcac ttccagaatt gccaccattt tcgatttttt aattcttgat tttctagtaa
     1081 caactgatcg tttttttgtt gctgaagcaa agtcaatttt tgttggtcac gaatcatttc
     1141 cgttaattca gaaatatgcc tatctttttc cgctaattgt tcacgcaaaa attcattttc
     1201 tttttctaac gggaaatcat tgcctgcatc attgaccggt aaatcaccag tcaattgacc
     1261 accttttgac cgataaattg accgcacaac accaatcaat tccttgtcta acatgataac
     1321 cccattatct ttataccgag caaggtcata acctgcattg accagttgat tgcgcactgt
     1381 atttttagat atacccaact catcagcaag gttttttatg gtcatttttt ctggcaaatc
     1441 agtcattatc ttctccgtta ctttcagcta ccccataaac atatttaaca gcatgcttag
     1501 ggataatgat tggggaatca attttattat ttttcaaaat caactcatac tgcgttacat
     1561 caagtaactt accggacatt tttttgctat ccaaaaaaac aacgacaacg ttatcacctg
     1621 ttaaattcac caaccaattt ttcttaccaa aatgcttttg tttttctgcc attcttattc
     1681 ctcctccgtt acatctaacc cttgaagcca agtgtctaat tcttttttca aaacatctgc
     1741 tgattccgaa aatgtttctc gtaaatgatt cgtcaactca tcattttgac tttctctttt
     1801 caaaatatct ctcaatttgt atttcattct acgctctaaa aacccccaca tttcagggtt
     1861 agcaatcagt ccaaaaatca tcaccttatc atttgttttt acatcaagtg gtagaaaatg
     1921 agggctagca aaactattta aactttcatg aaccattgca tgccaatctg ttgctttccc
     1981 acgccttaac tgcaattcca gtcgccacca agtttctatt tctggtggca caattttacg
     2041 cttggtttcc tgttccaatt ttttgttgta tagccgaatc tggcgttcgc tggcacgact
     2101 gccccaataa gctgtttcca gcttcccaga ccgcccataa attggcttga aagaaacagg
     2161 atcaaccact cgatattgtg taataaactc atcaggcaca tcgataatat cgcaagcaat
     2221 atccgcacgt gagaaatgtg gttctagaaa taaatcatga atgaaatttt tcattgaact
     2281 agctaaaaaa tgaccaatct tattcgggtt aaaatcaatc cgccctttgc catcttgcca
     2341 tttcaaaatc tcaatataag caatattttc ttcgtattgg tctaataatt gccagccgtt
     2401 attcccaacc gcttttaaat agccattgcc ttcattcacc cgcattaatt gctcaaaatc
     2461 taaaatcaac acatcatttt gagtgtgata ataaatattt tccttcagtt ttccaacgat
     2521 agtaattcgg tcaattgacc actgtaattt taggggggtg ttcaaatttt gaacatttaa
     2581 ccgcctgtta gatagggctg ttaaattttc ccactcattt acgattatgc catttttact
     2641 caaattttgt tcctcctcaa agaaaaagag acttctggaa agaattttca aaagttcacg
     2701 taactcttaa aaattcatta ccaaaaaatc tctagtcttg aagaaatcta aaaatattcg
     2761 tataatgatt aagaagttac ggagctagtg cgattagttt ccgtaaaggt cgagaacgtt
     2821 ggtagcgttg ctcgactatt tttttactct tttttcagtt catttgtttg ctaactcaat
     2881 aatagcactt ctctttagct atgcaaatat ccaaaaaata aaaccgcacc ctttgaaaag
     2941 ggcgccccca aacttcgcta acgctaggtt ggccaaaaaa tggactggcc attttttagc
     3001 aaatgtcagc ttaataggct agtggtttag ccgtcaactc cttatcctcg gcacaaaccg
     3061 cctccggtac cgttgactgc acatcgtaac taccactcga tctcatcttc agaacgctct
     3121 aatttacgct gtgagacgtt ttgacgataa aataaggttt tctcctgctc taacacttct
     3181 aattcctcag aaagccccat atccttttct gcaagaccaa aacggataga caaacgagtg
     3241 atcgattttt gaaatgcgtt ttttaatcgc tctaaacgct ggcgtaaaga gcgattttct
     3301 tctttcagct ttttattttc cacttgtaaa tctgctaatt gttttctacc agacaaatga
     3361 cgctcttctt ccaatgtagc tacatactca tttaattctg tattttgctc aagcatctgt
     3421 aaatattgct cactcatgtt atcagcattt ctcttggcat ttgttgctct cgtagctcgt
     3481 tgatacaaat caacaaaatc attcccagat aaatgatacg aaccatcagg aagcctcttg
     3541 aaactttcta aaggaaccat atctttttgg aaaatgaccg ccatctcttt ttttacattc
     3601 agcatatttt tcttctcttc ttcaatcttc gctctctcag aagccatcag agccttatca
     3661 cgctcgtttt cttctctttg cctataaata tacctcaact catcagaaac gctctcacgc
     3721 tcttttacag ccgtttggcg caattcagaa atttcactca tgatttcttt gtattcgtga
     3781 atatctttaa ttttgttggt accgacaata tcccttttcc aaccgtaatc attcattaat
     3841 cgttctatag agtcaacttc ttgatttcta aaattattga aaagcactcg accattatct
     3901 ttatcagcgt gtatcccttg ttgaaccagt gctttattaa agctcggctg cttttgaaca
     3961 ccccgtttat aaccttcagc aaccggcaca atattcaagt gcaggtgcgg acttatttcg
     4021 tcattatgaa taacagcatt ataaacagcc aaattagggt ttctctcttg aaactccttg
     4081 taatactgaa ccaaaatttt attggcaatc actcgatttt gttcagcttg ttgtttcgat
     4141 atgccagtag aagaaccatc tgctcgattt gtctggaaat catctaaaat gcctatttgc
     4201 acaataaatt ctcgttgagg ttccaacttt ttatccttgc gcactttcgc taaatagtcc
     4261 tcgatttttc tatcggctct tttttgtttc gcattatatt tttctaccac ttcgccaaac
     4321 aattcctcat atttatctgc tagattcgtc tgctctaaat aaatattttc atcc
//
