LOCUS       NZ_CP044279             4461 bp    DNA     circular CON 10-NOV-2023
DEFINITION  Enterococcus faecium strain V2937 plasmid pHVH-V2937-5, complete
            sequence.
ACCESSION   NZ_CP044279
VERSION     NZ_CP044279.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN12818041
            Assembly: GCF_008728475.1
KEYWORDS    RefSeq.
SOURCE      Enterococcus faecium
  ORGANISM  Enterococcus faecium
            Bacteria; Bacillota; Bacilli; Lactobacillales; Enterococcaceae;
            Enterococcus.
REFERENCE   1  (bases 1 to 4461)
  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  JOURNAL   Unpublished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 4461)
  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                   :: 69.0x
            Sequencing Technology :: Illumina MiSeq; Oxford Nanopore MinION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 11/10/2023 05:32:25
            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)                     :: 3,145
            CDSs (total)                      :: 3,050
            Genes (coding)                    :: 2,940
            CDSs (with protein)               :: 2,940
            Genes (RNA)                       :: 95
            rRNAs                             :: 7, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 7, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 70
            ncRNAs                            :: 4
            Pseudo Genes (total)              :: 110
            CDSs (without protein)            :: 110
            Pseudo Genes (ambiguous residues) :: 0 of 110
            Pseudo Genes (frameshifted)       :: 44 of 110
            Pseudo Genes (incomplete)         :: 65 of 110
            Pseudo Genes (internal stop)      :: 22 of 110
            Pseudo Genes (multiple problems)  :: 16 of 110
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP044279.1.
            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..4461
                     /organism="Enterococcus faecium"
                     /mol_type="genomic DNA"
                     /strain="V2937"
                     /isolation_source="Rectum"
                     /host="Homo sapiens"
                     /db_xref="taxon:1352"
                     /plasmid="pHVH-V2937-5"
                     /geo_loc_name="Denmark:Copenhagen"
                     /lat_lon="55.67 N 12.56 E"
                     /collection_date="2018"
                     /collected_by="Copenhagen University Hospital Hvidovre"
     gene            475..648
                     /locus_tag="F6440_RS16300"
     CDS             475..648
                     /locus_tag="F6440_RS16300"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_002341717.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_002318189.1"
                     /translation="MLKKTVLVLGSISLGILGFSPMLLSVIGKNNSNRELKLNSNYYNS
                     PNEELFVKETDK"
                     /name="hypothetical protein"
     gene            1053..1487
                     /gene="bacA"
                     /locus_tag="F6440_RS16005"
                     /old_locus_tag="F6440_16005"
     CDS             1053..1487
                     /gene="bacA"
                     /locus_tag="F6440_RS16005"
                     /old_locus_tag="F6440_16005"
                     /inference="COORDINATES: protein motif:HMM:NF041453.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="bacteriocin 51 precursor BacA"
                     /protein_id="WP_002351079.1"
                     /translation="MKNKIIKIITCLFLFGMIVGASTPLNLFPFSARGIKVEAASSRYN
                     HNHRGFTCYKMNYYVTNKMCRDLKKNYNKLKTPAQIASFIPIGGVGTWVITNAFSSAVD
                     AMNVFVRAANQGKGVQLTYNAHFSNTTSYQYNDYARYVIK"
                     /name="bacA"
     gene            2777..3700
                     /locus_tag="F6440_RS16010"
                     /old_locus_tag="F6440_16010"
     CDS             2777..3700
                     /locus_tag="F6440_RS16010"
                     /old_locus_tag="F6440_16010"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_002296860.1"
                     /GO_function="GO:0003887 - DNA-directed DNA polymerase
                     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 protein"
                     /protein_id="WP_002351085.1"
                     /translation="MANEIVKYENRLNHIPLRKFNSREMNLFFSIASRVREKGVDEIIF
                     SFHDLKKLSGYTERGEQFIKDLSSTYDKLLSINAWNDDGNTLTKFVAFTKYSIIRDKQL
                     VIISVNPEFKGLFNQLKNWTRFNLEQFTNLDSTYSKTMFRLLKQYRTQGWTEFSKEKFF
                     DLLDIPKSYWNSPSNIDKFILRPIKEELTPLFKGLTIRKKYGKGRGKPVIGYRFTWKAE
                     INHADDFSKGKQEDLRIKLFNIDHNGELTREEKWRAKDRILNLPLGTHEADFKQQQQTE
                     EKQAEKRELSNKLKQDLLGNLQNLFD"
                     /name="replication initiation protein"
     gene            3716..4255
                     /locus_tag="F6440_RS16015"
                     /old_locus_tag="F6440_16015"
     CDS             3716..4255
                     /locus_tag="F6440_RS16015"
                     /old_locus_tag="F6440_16015"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_016616811.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="DUF536 domain-containing protein"
                     /protein_id="WP_002351084.1"
                     /translation="MADKTIKELAEELGVSKTAINKKVSDKNRKLWFAKNGNKFVINET
                     GQKAIKSMFLVDNANLNRKLVGEKSKTKNHKNTNQVSELKLLSFLEKQLNRKDIQLQEK
                     DNQIKQMQKLLDQQQQLTLQANQQIENLQEQLHLTYTEETPTTESTAFSEKKADNTQPL
                     IEKKWWQIWKSNRTNL"
                     /name="DUF536 domain-containing protein"
     Typing          2778..3700
                     /name="rep_cluster_1291"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 tctaatcgat tttgttgaaa aagtcataaa aaaacaaatg tgattttaac aaaatttcaa
       61 aaaaatcgtt tgaaatttcg tttatttttt ttgagaattt tgatcatcgt agggtcattg
      121 tagaatcatt atgagatcat cgtgggatca tcgaataaag tatgggaaag gcttgcggtg
      181 cttggtatta agggcattct ccgcctccca ggttcttgac cattttctct tataagtggg
      241 atttttacca cgttgagaga aaatggtcaa gaacctggga ggcggagaaa acataccaag
      301 caccacaagc aaaaaaagtt agagtaactt ccaaaaaaga aaaatttttt agaacaactt
      361 ttgaaaattt aattttgatt tatatccgtt caatttaaac atttgataaa ctgaaggcta
      421 gtatttaaaa tgtgtataca agtggtagcg ttaaaaaaag tggaggtata acctatgtta
      481 aaaaaaactg tgttggtact gggttctatt tctctaggaa tattaggttt tagccccatg
      541 ctattatccg taattggaaa aaacaattcc aacagagaac ttaaattgaa ttcaaattat
      601 tacaacagtc ctaacgaaga attgtttgta aaagaaacgg ataaataata aaaaagactg
      661 ctcttccgag cagccagtta aaaaataatg agtgtttatt cttgaaaaag caacgcgctt
      721 ataaagcgct accaaaaatt tatcatattt tatgaaaaat aacaatccag taaaaaatga
      781 ctggtaaaaa ttcacaaaga aacggaaaga agcaactgca gaaaatcaag ccttaaaaag
      841 agctttttac ctagaccaat taaaaatcac aaagtgagcc cctgtatcgg ttgatacaag
      901 ggctacttgg catactgtac attatgtcta ctaaccttta aaataacacg ttttataaaa
      961 taaaccctct tgacaatatt taattttctg attattctaa atatatacag aaagcgcttt
     1021 cctaggattt tatatctaag gaggaagtaa caatgaaaaa taaaattatt aaaattatta
     1081 cttgtctatt tttgttcggt atgattgttg gagcaagtac tccgttaaat ctgtttcctt
     1141 ttagtgctag aggtataaaa gtggaagctg caagttcacg atataatcat aatcatcgtg
     1201 gatttacttg ctataaaatg aactattatg ttactaataa aatgtgtaga gatttgaaaa
     1261 aaaattataa taagctaaag actcctgctc aaattgcatc ttttattcct attggtggag
     1321 ttggaacatg ggttattaca aatgctttta gtagtgctgt tgatgcaatg aatgtctttg
     1381 taagagctgc aaatcaagga aaaggtgtac aattaacata taatgctcac tttagcaata
     1441 caacatcata tcaatacaat gattacgctc gttatgtaat aaaataatca gaaagtgaaa
     1501 ctatctcatg aataaaaaga ttttagctgt aattatttca ataatagttt taatcactat
     1561 gttcttcata tttaggctaa ttttcaatat aagcttacaa aaaagtattc tttatctaat
     1621 tcctatagca tttatcttag caatttttag aagtatttac ggaaataaaa actctaaata
     1681 gctaaaaata aatcatacta aattttacaa aaagtggcta gcattttcta gccacttttt
     1741 gtattgtgga gcgtgggttt tgagggggat tcaaggggga gcttgcgccc ctttgacaag
     1801 cggttatttg caccaaatac ggaggtattt ggctagcaaa tatagagctt gccaaaccct
     1861 tttagtgagt tttgtagaaa gtacctttaa aggtactttc acattacgaa cgatacgtcc
     1921 gtaggacgta ctgaaagggt gggacttatg agcaaattaa tgcaaaattt ggctagcaaa
     1981 aaagctaaaa aatatatgct aataatcgag cgaaataaac actttttcaa gtgagcgaat
     2041 ccgccatgac aaagctgaag cagtttattt cagctttgtc atggcgtgtg ccgacttttt
     2101 taaaagtcta ggcacacgag caaatatctt tatcaagctc taatttgcgt tttaagacgt
     2161 ttgaaacgcc taagtatata aatatataag aataggttta agagtgctta aatcgaattt
     2221 tagagggcat ttagacaatt ttagggttgt tagggcttgc cctgaccgcc tgtaaggcgt
     2281 tttaagaaca agataaggga tttatactag gactgtctta aaatgtctta aacgaacgct
     2341 cagagcttct caaagggttc cttatgaacg gcttttagca aaggagccgg aggcgactgc
     2401 gcagtataat gtgagagcag agcgatcaca cctttttagc gaaccgtagg gagcaaggtt
     2461 tggaattggc agttttgata aattcgcgaa cctgtttaga gaaaaaagga gtgatttttt
     2521 aggcgggaaa attagcctcc cctcttttta tatctctttt tatatctctt tttatatctc
     2581 ttttatgtcg gctgtgtcct tactctccca agcaattcag agttttttca agtaggtttt
     2641 ctacgctttt caagtaggtt ttctacgctt ttcaagtagg ttttctacgc ttttcaagta
     2701 ggttttccga cattattgag tatttttata aagtatgtta cttttatttc atactttata
     2761 aaagtaggag aagcttatgg caaatgaaat tgtaaaatat gaaaatagat taaatcatat
     2821 tcctctgaga aaatttaata gtcgtgaaat gaacttattt ttttcaattg cttcacgtgt
     2881 acgtgaaaaa ggtgtagatg agattatttt ttcatttcac gatttgaaaa aactaagcgg
     2941 ttatacagaa cgtggggaac aatttataaa agatcttagt agcacgtatg acaaattatt
     3001 aagtattaat gcttggaatg atgatggaaa tactttaact aaatttgttg ctttcacaaa
     3061 atatagcatt atacgagata aacaacttgt tataatttca gttaatccag aatttaaagg
     3121 actttttaat caattaaaga actggacaag atttaatcta gagcaattta ctaatttgga
     3181 tagcacatat tcaaaaacta tgtttcgatt attaaaacaa tatcgaactc aaggctggac
     3241 tgaattttcc aaagaaaaat tttttgattt actagatatt cctaaaagtt attggaatag
     3301 tccgtcaaat attgacaaat ttatcttaag gccaattaaa gaagaactca ctcccttatt
     3361 taaaggatta actattcgta aaaaatatgg taaaggtcga ggtaaacctg ttatcggtta
     3421 tcgttttact tggaaagctg aaattaacca tgctgacgat ttttccaaag ggaaacaaga
     3481 agatttacgt ataaaattat ttaatattga tcacaatgga gaattaacac gagaagaaaa
     3541 atggcgcgct aaagatcgaa tactaaatct tcccttaggc actcatgaag ctgattttaa
     3601 acaacaacaa caaactgaag aaaaacaggc agaaaaacga gaactttcaa acaaactcaa
     3661 acaagattta ctaggaaatt tacaaaactt attcgattaa gcttaaggag tatttatggc
     3721 agataaaaca atcaaagaac ttgcggaaga attaggagtt agtaaaacag caattaacaa
     3781 aaaagtttct gacaaaaatc gaaaactttg gtttgcaaaa aacggaaaca agtttgtgat
     3841 taacgaaacc ggtcaaaaag ctataaaatc aatgttttta gtcgataacg caaacttaaa
     3901 tcgaaaacta gttggcgaaa aatcaaaaac caaaaaccat aaaaacacca accaagtttc
     3961 cgaattaaaa ctcctttctt tcctagaaaa acagttaaat cgaaaagata tacagctaca
     4021 agaaaaagat aatcaaataa aacaaatgca aaaattactc gaccagcaac aacaactcac
     4081 tctacaagcg aaccaacaaa ttgagaacct acaagaacag ctccatttaa cttatacaga
     4141 agaaactcca acaaccgaat caactgcctt ttctgaaaaa aaagcagaca atacacaacc
     4201 acttattgaa aaaaagtggt ggcaaatttg gaaatctaat agaaccaatc tctaaaattt
     4261 tctagaagtt agttcggata gtagaggaaa aagttgtact acctgatggg gagatcactc
     4321 aaatttttat gagaaagaaa aaatagttta caactgtaaa caatcaatgt ttatagttgt
     4381 aaactatcaa actatatggt gacttattgc ttaaaatagg ttgaaatctc actcaatttt
     4441 tggtggaaaa acaaaataaa t
//
