LOCUS       NZ_CP083917             2947 bp    DNA     circular CON 05-NOV-2023
DEFINITION  Enterococcus faecium isolate V1225 plasmid pV1225-5, complete
            sequence.
ACCESSION   NZ_CP083917
VERSION     NZ_CP083917.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMEA5367970
            Assembly: GCF_020162155.1
KEYWORDS    RefSeq.
SOURCE      Enterococcus faecium
  ORGANISM  Enterococcus faecium
            Bacteria; Bacillota; Bacilli; Lactobacillales; Enterococcaceae;
            Enterococcus.
REFERENCE   1  (bases 1 to 2947)
  AUTHORS   Mollerup,S., Elmeskov,C., Gumpert,H., Pinholt,M., Sejersen,T.S.,
            Pedersen,M.S., Worning,P., Frees,D. and Westh,H.
  TITLE     Rapid in vivo development of resistance to daptomycin in
            vancomycin-resistant Enterococcus faecium due to genomic
            rearrangements
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 2947)
  AUTHORS   Mollerup,S., Elmeskov,C., Gumpert,H., Pinholt,M., Sejersen,T.S.,
            Pedersen,M.S., Worning,P., Frees,D. and Westh,H.
  TITLE     Direct Submission
  JOURNAL   Submitted (17-SEP-2021) Department of Clinical Microbiology,
            Copenhagen University Hospital Hvidovre, Kettegaard Alle 30,
            Hvidovre 2650, Denmark
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Date                     :: 27-MAR-2019
            Assembly Method                   :: Unicycler v. 4.0.7
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 154x
            Sequencing Technology :: Illumina MiSeq and Oxford Nanopore MinION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 11/05/2023 01:46:48
            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)                     :: 2,991
            CDSs (total)                      :: 2,899
            Genes (coding)                    :: 2,745
            CDSs (with protein)               :: 2,745
            Genes (RNA)                       :: 92
            rRNAs                             :: 6, 6, 6 (5S, 16S, 23S)
            complete rRNAs                    :: 6, 6, 6 (5S, 16S, 23S)
            tRNAs                             :: 70
            ncRNAs                            :: 4
            Pseudo Genes (total)              :: 154
            CDSs (without protein)            :: 154
            Pseudo Genes (ambiguous residues) :: 0 of 154
            Pseudo Genes (frameshifted)       :: 73 of 154
            Pseudo Genes (incomplete)         :: 75 of 154
            Pseudo Genes (internal stop)      :: 41 of 154
            Pseudo Genes (multiple problems)  :: 32 of 154
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP083917.1.
            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..2947
                     /organism="Enterococcus faecium"
                     /mol_type="genomic DNA"
                     /isolate="V1225"
                     /isolation_source="Hospitalized patient"
                     /host="Homo sapiens"
                     /db_xref="taxon:1352"
                     /plasmid="pV1225-5"
                     /geo_loc_name="Denmark"
                     /collection_date="2015"
     gene            complement(join(2118..2947,1..145))
                     /locus_tag="LCG89_RS14845"
                     /old_locus_tag="LCG89_14845"
     CDS             complement(join(2118..2947,1..145))
                     /locus_tag="LCG89_RS14845"
                     /old_locus_tag="LCG89_14845"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_002342725.1"
                     /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_002337993.1"
                     /translation="MSKRGTIINEWEKLNRISNRRLNAQTMCTPLKMQWSIDRITIVGT
                     LRENIYYHTPHDVLILDFEQLMRLNEGNGYLKAVGNNGWQLLDQHEENIAYIEILKFQE
                     GKGRIDFNPNKISQFLAGSMKNFIHDLFLEPHFSRADIACDIIDVPDDFITQYRVVDPV
                     SFKPIYGRSGKLETAYWGSRASERQIRMYNKKLEQERKRKVVPKEIDTWWRLELQLRRG
                     KATDWHAMVHESLDSFASPHYLPEDVKVTDRMMITALITEHSYWGQIHRNSKYKYRELL
                     KQESQNDELTNHLRETFSESADDLKRELDTWLQGLDVTEVGAE"
                     /name="replication initiation factor domain-containing
                     protein"
     gene            945..1226
                     /locus_tag="LCG89_RS14850"
                     /old_locus_tag="LCG89_14850"
     CDS             945..1226
                     /locus_tag="LCG89_RS14850"
                     /old_locus_tag="LCG89_14850"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_002347307.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_002347307.1"
                     /translation="MDILVRKIDSKVIAKIDKRCQELTNKTGKKWSRNRYLKVLIENDF
                     DHALMHYKKDQFDLLLEKFIAIQEKNTETLNEYVRTNNQLIETLIGGR"
                     /name="hypothetical protein"
     gene            1228..1644
                     /locus_tag="LCG89_RS14855"
                     /old_locus_tag="LCG89_14855"
     CDS             1228..1644
                     /locus_tag="LCG89_RS14855"
                     /old_locus_tag="LCG89_14855"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001232859.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_002322684.1"
                     /translation="MRKTSVQKHVTLYPSHVDVLDSIIERNPDINNYSEAIRFLCMSYE
                     PDTNTTTTSNQAKLNAMGKEISIMSEIIAEFADLYLKDTGILIGTNSKVYQETKEKIEK
                     QLNPSKRNQPKNRQKETNQTFTSKNFDPTNFLKR"
                     /name="hypothetical protein"
     gene            complement(1981..2121)
                     /locus_tag="LCG89_RS14860"
                     /old_locus_tag="LCG89_14860"
     CDS             complement(1981..2121)
                     /locus_tag="LCG89_RS14860"
                     /old_locus_tag="LCG89_14860"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_002326822.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="DeoR family transcriptional regulator"
                     /protein_id="WP_002322683.1"
                     /translation="MSDSIEKMTLKKLADELGVSKNTVRNQLVNSGFDLAQYKEKNAVV
                     N"
                     /name="DeoR family transcriptional regulator"
     Typing          complement(2122..2947)
                     /name="rep_cluster_943"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="82.754"
                     /coverage="87.0"
                     /evalue="0.0"
ORIGIN
        1 tttcccttaa tgtaccaaca atggtaattc ggtcaattga ccattgcatt tttaaggggg
       61 tgcacatagt ttgtgcattt aaccgcctgt tagatatgcg gttaagtttt tcccactcat
      121 ttatgatcgt gccacgttta ctcaaatttt gttcctcctc aaagaaaaaa gagatttttg
      181 gaaagaattt ccagagttca cgtaactcta aaaatccata tccaaaaatc tctagcttga
      241 agaaacctaa aaatattcgt ataatgaatt tgagttacgg aactaggtga gtagtttccg
      301 taattagccg aagggtgctt ccaacaccgt tcggctttta ttttgctctt ttttctcgtt
      361 ttctttgatt atagcactcc tcttaaaaaa ataaaaagac ctcagggaat ttcattcccc
      421 gaaccccttg agcctcctcc tgccgaaatt atttcacgct tccgctcttc atttcattca
      481 gttctcggct tgcacaatct aacacgccgt ttcgctacca gtcgccttac aggctccatt
      541 ctcgcttctc ttacgtgttt taacgattgt gccgataact aaacgaaatg aacgctaaaa
      601 cgtcttagaa cgcaaaatac gcgcttataa aatcatttca tcttgattac atgcccgtca
      661 taatcgttca gtttagtttc attttcgtaa acttttttta tttttacgaa cagaaaaaag
      721 tcgcacatca ccattttata aagagcataa ggaaacgtgt acccactttc taaaaaaagt
      781 gggtagatag gctgtgccta tcacgtttct cagaaaaaaa tttgatatca ctttttcgcc
      841 atcgtggcta gcttatgtat agtattttag caaaaaacag ctatacaaat actatattcg
      901 tatgatatac ataaattata cacaaatgcg aaaggagttt ttctatggac attttagttc
      961 ggaagatcga ttcaaaggtt attgcaaaaa tagacaaacg ttgccaagaa ctcacaaata
     1021 aaactggcaa aaaatggagt cgaaatcgct acttaaaagt cctaatcgaa aacgattttg
     1081 accacgcact tatgcattac aagaaagatc aattcgattt attactcgaa aaatttatcg
     1141 ctattcaaga aaaaaatact gaaacgctga atgaatatgt tcgtacaaac aaccaactca
     1201 ttgaaacact tatcggagga agataacatg agaaaaactt ctgttcaaaa acacgttacc
     1261 ctttatccca gtcacgtgga cgttttagat tccattatcg aaagaaatcc agatatcaac
     1321 aattactcgg aagccattcg ttttttatgt atgagttatg aacctgatac caatactacg
     1381 actaccagca accaagccaa actaaatgct atgggaaaag aaatttccat catgtccgaa
     1441 atcattgcag aatttgctga tttatatcta aaagatacag gtattcttat tggcacaaat
     1501 tctaaagtgt atcaagaaac gaaagaaaaa attgaaaaac aacttaatcc ctccaaacga
     1561 aatcaaccaa aaaatcgtca aaaagaaacc aatcaaacat ttacttctaa aaatttcgac
     1621 ccaacaaatt ttctaaaaag ataaaaaata aaccaggaga tttaaattcc tggtttattt
     1681 tttgggtagg atcaccatct taatagcaac atttacaata agatagtaac caattgaatg
     1741 aaaaaaacga atttcagaag aaataacaga aaaaaagata aaaacaaaaa aattataaat
     1801 acatgatttg aattcataat cgtaaaaaaa gctgctcgta cgagcagcta aataagaaaa
     1861 agattggtat gttttaagga taaaataagt ataacaaatt tttcacatag agcaaagggg
     1921 gcgaaaatcg cccccttttt ttcgttttaa aaccccaaaa cccaaagaca taaatttcgg
     1981 tcaattgacc actgcatttt tttctttata ctgagcaagg tcaaatcccg aattgaccag
     2041 ttgattgcgc accgtatttt tcgatacacc caattcatca gcaagttttt ttagggtcat
     2101 tttttctatc gaatcactca ttcagcacct acttccgtca catcaagtcc ttgaagccat
     2161 gtatctaatt ctcgtttcaa atcatctgcc gactccgaaa atgtttctcg caaatgattc
     2221 gtcaactcat cattttgact ttcttgcttt aacaattcac gatatttata ttttgaattt
     2281 ctatgaattt gcccccagta actatgttcc gttataagag cagtaatcat cattctgtca
     2341 gttactttca catcttctgg caaatagtga ggacttgcaa agctatctaa actttcatga
     2401 accattgcat gccaatcagt tgctttcccc cttcgcaatt gcaattctag tcgccaccaa
     2461 gtatcgattt ctttcggaac aactttccgt tttctttctt gttccaattt tttgttatac
     2521 atccgaatct gtcgttcact agcacgactt ccccaatatg ctgtttccag tttcccagac
     2581 cgaccgtaaa ttggtttgaa agaaacagga tcaaccaccc gatattgggt aatgaaatca
     2641 tctggcacgt caataatgtc acaagcaata tctgcacgtg agaaatgtgg ttctaaaaat
     2701 aaatcatgga taaagttctt catcgagccc gccagaaatt ggctaatttt attggggtta
     2761 aagtcaatcc gcccttttcc ctcttgaaac ttaagaatct caatataagc tatattttcc
     2821 tcatgttggt ctagtaattg ccagccatta tttccaaccg cttttaaata tccgttacct
     2881 tcgtttagac gcataagctg ttcaaaatct aaaatcaaca catcatgggg agtgtgataa
     2941 taaatat
//
