LOCUS       NZ_CP044270             5569 bp    DNA     circular CON 10-NOV-2023
DEFINITION  Enterococcus faecium strain V1836 plasmid pHVH-V1836-6, complete
            sequence.
ACCESSION   NZ_CP044270
VERSION     NZ_CP044270.1
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 5569)
  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  JOURNAL   Unpublished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 5569)
  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
            CP044270.1.
            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..5569
                     /organism="Enterococcus faecium"
                     /mol_type="genomic DNA"
                     /strain="V1836"
                     /isolation_source="Rectum"
                     /host="Homo sapiens"
                     /db_xref="taxon:1352"
                     /plasmid="pHVH-V1836-6"
                     /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(5471..5569,1..357))
                     /locus_tag="F6439_RS16600"
                     /old_locus_tag="F6439_16600"
     CDS             complement(join(5471..5569,1..357))
                     /locus_tag="F6439_RS16600"
                     /old_locus_tag="F6439_16600"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_002334263.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="LMxysn_1693 family intestinal colonization
                     protein"
                     /protein_id="WP_002322959.1"
                     /translation="MKKQLFKTFLLSTSILTFGSAITPSGAVFANENNISDIATYSDDE
                     YYYVLDEPVIQTRTWSKPQSWSIAKGSRTYLGIETHSRGTKLSVSANVFGMKIEIARNT
                     SASGKFKKYRQNARITVTYRVYRKVDNKYIRTQTSTANTQYIDYIPA"
                     /name="LMxysn_1693 family intestinal colonization protein"
     gene            complement(977..1393)
                     /locus_tag="F6439_RS16605"
                     /old_locus_tag="F6439_16605"
     CDS             complement(977..1393)
                     /locus_tag="F6439_RS16605"
                     /old_locus_tag="F6439_16605"
                     /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_002305824.1"
                     /translation="MRKTSVQKHVTLYPSHVDVLDSIIEKNPDVNNYSEAIRFLCMSYE
                     PDTNTTTTSNQAKLNAMGKEISIMTEIMAEFADLYLKDTGVLIGTNSKVYQEVKEKIEN
                     QLNPSRRNQPKNRQKETNQTFTSGNFDPTNFLKR"
                     /name="hypothetical protein"
     gene            complement(1395..1676)
                     /locus_tag="F6439_RS16610"
                     /old_locus_tag="F6439_16610"
     CDS             complement(1395..1676)
                     /locus_tag="F6439_RS16610"
                     /old_locus_tag="F6439_16610"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000353845.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_002347613.1"
                     /translation="MDILVRNINPKIIARIDKRCQELTTKTGKKWSRNKYLKVLIESDF
                     DRQLMNYKKDQFDLLLEKFIAIQTENTNILNDYVHTNNQLIETLIGGI"
                     /name="hypothetical protein"
     gene            complement(2052..2576)
                     /locus_tag="F6439_RS16615"
                     /old_locus_tag="F6439_16615"
     CDS             complement(2052..2576)
                     /locus_tag="F6439_RS16615"
                     /old_locus_tag="F6439_16615"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_002305828.1"
                     /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_044383356.1"
                     /translation="MTEKTIKELAEELGVSKTAINKKVSDENRKLWFSKIGNKFVINET
                     GQKAIKSMFFNENENSNQQLVGEKTKTENHKNANQVPELEVLSLLEQQLNQKDMQLQEK
                     DEQIKQMQKLLDHQQQLTLQANQQIEKLQEQLQLTYTEESSENKSTTLSEETESIEKQS
                     KAEKKWWQFWQ"
                     /name="DUF536 domain-containing protein"
     gene            complement(2593..3561)
                     /locus_tag="F6439_RS16620"
                     /old_locus_tag="F6439_16620"
     CDS             complement(2593..3561)
                     /locus_tag="F6439_RS16620"
                     /old_locus_tag="F6439_16620"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_002347614.1"
                     /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_002347614.1"
                     /translation="MSNEIVKYHHELNTIPLRKFTPVEMNLFFSIVSRMRDVGDKKVQF
                     TFEQLKDLSNYKATANVRFIDDLETTYDKLMDLRFGRRSADGLQRERFVLFNQFKIDGK
                     SDIPFAEIQVHEKALPLLNNLEEWVRYSLQQFNELESSYSKTMFRLLKQYRTKGFAYFS
                     KEDFHELLDIPKSYNQGTIDQRVFNPIRQELTAIFKGLTIKKKYGKGRGKPVIGYQFTF
                     KPEIKKSDDFNKHAPTKEEQNKALELANQQVQSEKAPTSLQEKIKEQKRKLELLQQLEK
                     LEREQNTQNKENNAQKSEINSDIPSELKKDLLDNLQNLFKD"
                     /name="replication initiation protein"
     gene            complement(4728..4883)
                     /locus_tag="F6439_RS16895"
     CDS             complement(4728..4883)
                     /locus_tag="F6439_RS16895"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_016631617.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_162846310.1"
                     /translation="MKLTKLTISLVIIAGIILYFVLPANQFFLYFGIPTILIVNGVRIF
                     EQRKKM"
                     /name="hypothetical protein"
     gene            complement(4902..5471)
                     /locus_tag="F6439_RS16630"
                     /old_locus_tag="F6439_16630"
     CDS             complement(4902..5471)
                     /locus_tag="F6439_RS16630"
                     /old_locus_tag="F6439_16630"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_002322960.1"
                     /GO_function="GO:0004222 - metalloendopeptidase activity
                     [Evidence IEA]"
                     /GO_process="GO:0071586 - CAAX-box protein processing
                     [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="type II CAAX endopeptidase family protein"
                     /protein_id="WP_002322960.1"
                     /translation="MTIKWIISIAYLVLTFAIPSLGVPSNIYFLFEHSDIFFLVLIIIL
                     FHSTFIREFKEVNLKKLFKYSFFSFSVLFLINILNTSFSEGINPNEVNGSLLLFFLNAA
                     TYGAFLEEGIFRFCMIDPQANKKQQYISILISSFLFSIVHGGGLSIFFIGIILSFVYIQ
                     TKNIWYSIVAHGFYNTIGILIYLISI"
                     /name="type II CAAX endopeptidase family protein"
     Typing          complement(2598..3561)
                     /name="rep_cluster_1093"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="93.782"
                     /coverage="99.0"
                     /evalue="0.0"
ORIGIN
        1 tattcttgca ttttgacgat attttttaaa ttttccactt gcagaagtgt ttctggctat
       61 ttcgattttc atcccaaata catttgcact gacagataac tttgtacctc gactatgagt
      121 ttctatacct aaataagtac ggcttccttt agcaattgac cagctttgag gtttagacca
      181 agtccttgtt tgaataactg gttcgtctaa cacatagtag tactcatcat cagaataagt
      241 ggctatatca gaaatgttgt tctcattagc gaataccgct ccgctaggag taatagcaga
      301 accaaaagtt aaaatagaag tagataataa aaaggtttta aataactgtt ttttcatcaa
      361 aatcacctcg aatataagat acttaagaaa acgctttctt tatataatta gaataatcag
      421 gaaatttaat gttgtcaaga gggtttattt tataaaagct gttatattaa aggttagtag
      481 acataatgta cactatgcca agtagcccct ctaccaatgg atagagacgc tcactttgtg
      541 atttttaatt ggtctagcta gttactagct tctaatgctt gattttacgc gatttctctt
      601 ttttagttct ttgtgcattt ttatctgtca ttttttaaag acttgttatt tttgagagga
      661 tttgatatgc tttttttgtc tttctctagt tcttcacttt gtaatatttt tatgttgatg
      721 aataggataa tctcattttg ggctgctcgt gagagcagtc tttttttgtt tcagggtacg
      781 tcctattctt tggatttccg cgctattaaa taaccgatac ttggggattg gggtagcgcc
      841 ccaaaataca aaaagaagaa gttgcataag cggatttttc ttttttttcg caagttggta
      901 ccaacttgca aatcttgctg gaagactgat ccctaaaaag aaatcgagga atttttttag
      961 ggatcggttt ctttttttat ctttttagaa agtttgttgg gtcaaaattt ccagaagtaa
     1021 aggtttgatt ggtttctttt tgacgatttt tgggttgatt tcgtcgggaa ggattgagtt
     1081 gattttcaat tttttctttc acttcttgat acactttaga atttgtaccg ataagaacac
     1141 cagtatcttt tagatataaa tcagcaaatt ctgccatgat ttctgtcatg atagaaattt
     1201 cttttcccat ggcattgagt tttgcttggt tactggttgt ggttgtattg gtatcaggtt
     1261 cataactcat acataaaaaa cgaatggctt ctgaataatt gttgacgtct ggattttttt
     1321 cgatgatgga atctaaaacg tcaacgtgac tgggataaag ggttacgtgt ttttgaacag
     1381 aagtttttct catgttatat tcctccgata agtgtttcaa tgagttggtt gtttgtgtga
     1441 acatagtcat tcagtatgtt cgtattttct gtttgaatgg caataaattt ttcgagtaat
     1501 aaatcgaatt gatctttttt gtaattcata agttgacggt caaaatcact ttcgattaga
     1561 acttttagat atttatttcg actccatttt ttgcccgttt tggttgtgag ttcctgacaa
     1621 cgtttatcta ttcttgcaat aattttggga ttgatatttc gaactaaaat gtccatggaa
     1681 attttccttt cgtatcagcg tataatttat gtataccata caaatatagt atttgtatag
     1741 ctatttttcg ccaaaacact atacatagcc tagccacaat ggcaaaaaag tgatagcaaa
     1801 tttttttctg agaaacgtga taggcacagc ctatctagca cctttcgtaa gaaagtgata
     1861 ccacgtttcc ttatgctctt tcaaaattca gaaaaatcag ctgtaaaacg agtgcagtcc
     1921 gagtaagatt caacgaaaaa acggggattg gggcgccacc aaaatatcgc aacatgggtc
     1981 catgttgctc tgctcgcaaa agcaaaaaga agaataaaac cagcaatttt tattaattta
     2041 aattgctggt tttattgcca gaattgccac cattttttct ccgcctttga ttgtttttct
     2101 atcgattctg tttcttcaga aagagtcgtt gatttatttt ccgaagattc ttccgtataa
     2161 gtcaactgta gttgttcctg cagtttctcg atttgttggt tggcttgcag ggtgagttgt
     2221 tgttggtggt cgagtaattt ttgcatttgt tttatttgct cgtctttttc ttgtagttgc
     2281 atatcttttt gatttaactg ttgttctagg agagaaagga cttctaattc gggaacttgg
     2341 ttggcgtttt tgtggttttc ggttttcgtt ttttcgccaa ctagttgttg atttgagttt
     2401 tcgttttcgt taaaaaacat tgattttata gccttttgtc cggtttcatt aatcacaaac
     2461 ttgtttccga ttttcgaaaa ccaaagtttt cgattttcgt cagaaacttt tttgttaatt
     2521 gctgttttac taactcctaa ttcttcagca agttctttga ttgttttttc tgtcataaaa
     2581 tctaaaaacc cctcaatctt tgaataagtt ttgaagattg tctaataagt ctttttttag
     2641 ttctgaagga atatcggaat ttatctctga tttttgtgca ttattttctt tattttgggt
     2701 attttgttct ctttctaact tttctaactg ttgtaaaagt tccaattttc gcttttgttc
     2761 tttgattttt tcttgtaatg aagtaggtgc tttttcagat tgaacttgtt ggttagctag
     2821 ttctaatgct ttgttttgtt cttcttttgt tggggcatgt ttgttaaagt cgtctgattt
     2881 ttttatctca ggtttaaatg taaattgata gccaatgaca ggctttcccc gtccttttcc
     2941 gtatttcttt ttgattgtta aacctttaaa gattgcggtt agttcttgtc gtattggatt
     3001 gaacacacgt tgatcaatcg taccttggtt gtaactttta ggaatatcaa gtaattcatg
     3061 aaagtcttct tttgaaaaat aagcgaaacc tttggttctg tattgtttta gtaatcgaaa
     3121 cattgttttt gaataactgc tttctaattc attgaattgt tggagagaat agcgcaccca
     3181 ttcttcaaga ttattaagta agggtaaggc tttttcatga acttgtattt cagcaaaagg
     3241 aatatcagat tttccgtcga ttttaaattg attaaataaa acaaaacgtt cacgttgcaa
     3301 accgtcagca cttcttctac caaaacgtaa atccattaat ttgtcatacg ttgtttctaa
     3361 atcatctatg aatcgaacat ttgcagttgc tttataattg cttaaatctt ttaattgctc
     3421 gaatgtaaat tgtacttttt tatcacctac atcacgcatt cttgatacga tagaaaagaa
     3481 caaattcatt tcgactggtg taaattttcg caacggaatt gtatttaatt catgatgata
     3541 ctttacgatt tcattagaca tatttaaaat agctcctttc ttactcgcac aagagataca
     3601 cgttatgaaa tacaaaatgc ctgtttatct acatcttata ttaacatcgt cgatgtacta
     3661 attcaatgta caaacagaca aaacgatgta gataaacaga caaaacgatg tagataaaca
     3721 gacaaaacga tgtagataaa cagacaaaac gatgtagata aaagcgtcat tcccttggga
     3781 gagtaaggat atagccgacg gtaaagaggt ttaaaaagag gtttaaaaag agattataaa
     3841 agagggggac aaaatttccc gcctaaaaaa ccacttcttt tttctccaaa cagattcgcg
     3901 catttttctc aactgggaat cttactccct acagtcgctt aaaaaggtgt gatcgctctg
     3961 ctctcacatt atactgcgca gtcgcttccg gctcctttgc taaaaatgtt cataaggaac
     4021 tctttgagaa gctatgagcc ttcgtttgag acgttttaag acagtcttag tataaatccc
     4081 ttatcttgtt cttaaagcgc cttacaggcg gtcagggcaa gccctaacaa ccctaaagtt
     4141 gtctgaatgc cctctaaaat tcgatttaag cactcttaaa cctactctta tatatttata
     4201 tacttagacg tttcaaacgt cttaaaacgc aaattagagc ttgataaaga tatttgctcg
     4261 tgtgccgact tttttaaaag tctaggcaca cgccatgaca aagctgaaat aaactgcttc
     4321 agctttgtca tggcggattc gctcacttga aaaagtgttc atttcgctcg attattagca
     4381 tatatttttt aacttttttt gctagccaaa ttttgcatta gttcgctcat aaatcccacc
     4441 ctttcagtac gtcctacgga cgtatcgttc gtaatgtgaa agtaccttta aaggtacttt
     4501 ctacaaaact cactaaagtg tttggcaagc tctatatttg ctagccaaat acctacgtat
     4561 ttggtgcaaa taaccgcttg tcaaaggggc gcaagctccc ccttgaatcc cccctcaaaa
     4621 cccacgctcc acaatacaaa aaaggctagc aaatgctagc cactttttgt aaagtttcgc
     4681 ttgtttcacc ttcggtgaaa ttgttgcttt gcaacgatca ggtagagcta catttttttt
     4741 cgttgttcaa atattcttac gccatttact attaaaatcg taggtattcc aaagtaaaga
     4801 aaaaattgat tagcaggtaa tacaaaatat aaaataatac cagcaataat taccaaactt
     4861 atagtaagtt ttgttaattt catgaagtat gccaccttat cttatataga tatcaaatag
     4921 attaatatgc cgattgtatt ataaaatcca tgagcaacta tggaatacca tatatttttt
     4981 gtttgtatat aaacaaaact taaaataata ccaataaaga aaatacttag gcctccccca
     5041 tgaacaatag aaaacagaaa agaagaaatt agtattgaaa tatattgttg ttttttgttt
     5101 gcttgaggat caatcataca aaatcgaaaa attccttctt ctaaaaaagc tccataagta
     5161 gcagcattta aaaagaataa aaggagagaa ccatttactt cattaggatt tataccttct
     5221 gaaaaagatg tatttagaat attgattagg aataaaacag agaatgaaaa aaaactatat
     5281 ttaaagagtt tttttagatt tacttctttg aattcacgaa tgaaggtaga atgaaatagt
     5341 ataattatta gcactaaaaa aaatatatca ctatgttcaa ataaaaaata tatatttgac
     5401 ggtactccta atgatgggat agcaaaggtc aaaaccaagt aagcaatact aattatccat
     5461 tttattgtca ttaggcagga atataatcaa tatattgtgt atttgctgta gaagtttgag
     5521 tacgaatata tttattatct accttacgat aaactctgta ggttacagt
//
