LOCUS       NZ_CP041275             5212 bp    DNA     circular CON 20-APR-2024
DEFINITION  Enterococcus faecium strain VVEswe-S plasmid pVVEswe-S6, complete
            sequence.
ACCESSION   NZ_CP041275
VERSION     NZ_CP041275.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN12138986
            Assembly: GCF_007917315.3
KEYWORDS    RefSeq.
SOURCE      Enterococcus faecium
  ORGANISM  Enterococcus faecium
            Bacteria; Bacillota; Bacilli; Lactobacillales; Enterococcaceae;
            Enterococcus.
REFERENCE   1  (bases 1 to 5212)
  AUTHORS   Wagner,T.M., Janice,J., Sivertsen,A., Sjogren,I., Sundsfjord,A. and
            Hegstad,K.
  TITLE     Alternative vanHAX promoters and increased vanA-plasmid copy number
            resurrect silenced glycopeptide resistance in Enterococcus faecium
  JOURNAL   J Antimicrob Chemother 76 (4), 876-882 (2021)
   PUBMED   33367710
REFERENCE   2  (bases 1 to 5212)
  AUTHORS   Wagner,T.M., Janice,J., Sivertsen,A., Sjogren,I., Sundsfjord,A. and
            Hegstad,K.
  TITLE     Direct Submission
  JOURNAL   Submitted (26-JUN-2019) Department of Microbiology and Infection
            Control, Norwegian National Advisory Unit on Detection of
            Antimicrobial Resistance, Sykehusveien 38, Tromso 9038, Norway
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Date                     :: JAN-2019
            Assembly Method                   :: Unicycler v. v0.4.6
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 252.0x
            Sequencing Technology             :: Oxford Nanopore MiniION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_007917315.3-RS_2024_04_20
            Annotation Date                   :: 04/20/2024 04:32:37
            Annotation Pipeline :: NCBI Prokaryotic Genome Annotation Pipeline
            (PGAP)
            Annotation Method :: Best-placed reference protein set; GeneMarkS-2+
            Annotation Software revision      :: 6.7
            Features Annotated                :: Gene; CDS; rRNA; tRNA; ncRNA
            Genes (total)                     :: 3,249
            CDSs (total)                      :: 3,156
            Genes (coding)                    :: 3,042
            CDSs (with protein)               :: 3,042
            Genes (RNA)                       :: 93
            rRNAs                             :: 6, 6, 6 (5S, 16S, 23S)
            complete rRNAs                    :: 6, 6, 6 (5S, 16S, 23S)
            tRNAs                             :: 71
            ncRNAs                            :: 4
            Pseudo Genes (total)              :: 114
            CDSs (without protein)            :: 114
            Pseudo Genes (ambiguous residues) :: 0 of 114
            Pseudo Genes (frameshifted)       :: 46 of 114
            Pseudo Genes (incomplete)         :: 63 of 114
            Pseudo Genes (internal stop)      :: 25 of 114
            Pseudo Genes (multiple problems)  :: 16 of 114
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP041275.1.
            Bacteria and source DNA available from Kres.
            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..5212
                     /organism="Enterococcus faecium"
                     /mol_type="genomic DNA"
                     /strain="VVEswe-S"
                     /isolation_source="feces"
                     /host="Homo sapiens"
                     /db_xref="taxon:1352"
                     /plasmid="pVVEswe-S6"
                     /geo_loc_name="Sweden:Halmstad"
                     /lat_lon="56.6744 N 12.8578 E"
                     /collection_date="2014"
                     /collected_by="Hospital of Halland"
     gene            complement(285..728)
                     /locus_tag="FLC01_RS15815"
                     /old_locus_tag="FLC01_16655"
     CDS             complement(285..728)
                     /locus_tag="FLC01_RS15815"
                     /old_locus_tag="FLC01_16655"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_002334327.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_002318191.1"
                     /translation="MGQYHYKLVNKPIALVMGLVLVLFLTSCSKKQEIQKTDLIPFLGT
                     WQTKDHSERLVITNLNTSKNIEQYTILVKENNHKIQIIDKNLNINEQVFIYKATNNLLT
                     LRSNKKQLDYTFSLDSPKKLVFILTTNDGTEGTAKPIEFFKAD"
                     /name="hypothetical protein"
     gene            complement(701..1201)
                     /locus_tag="FLC01_RS15820"
                     /old_locus_tag="FLC01_16660"
     CDS             complement(701..1201)
                     /locus_tag="FLC01_RS15820"
                     /old_locus_tag="FLC01_16660"
                     /inference="COORDINATES: ab initio prediction:GeneMarkS-2+"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GeneMarkS-2+."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_060800863.1"
                     /translation="MNYNKNLLSHIVYFNYIIIGVYHLNLTQRRGYFETQKENLSRSPL
                     FLDDWNSQIESKSLNQDQIIKYANYCGVYPKKVARILNLSEVQTQLRKGNAIYMGTAGY
                     GNYSNSRHALALFGWVNQGGYQTYYVWNPWYNYPTVISANAGPVTIPVPGGGFTWDNTI
                     TNW"
                     /name="hypothetical protein"
     gene            complement(1743..2159)
                     /locus_tag="FLC01_RS15825"
                     /old_locus_tag="FLC01_16665"
     CDS             complement(1743..2159)
                     /locus_tag="FLC01_RS15825"
                     /old_locus_tag="FLC01_16665"
                     /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(2161..2442)
                     /locus_tag="FLC01_RS15830"
                     /old_locus_tag="FLC01_16670"
     CDS             complement(2161..2442)
                     /locus_tag="FLC01_RS15830"
                     /old_locus_tag="FLC01_16670"
                     /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(2818..3342)
                     /locus_tag="FLC01_RS15835"
                     /old_locus_tag="FLC01_16675"
     CDS             complement(2818..3342)
                     /locus_tag="FLC01_RS15835"
                     /old_locus_tag="FLC01_16675"
                     /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_060800956.1"
                     /translation="MTEKTIKELAEELGVSKTAINKKVSDENRKLWFSKIGNKFVINET
                     GQKAIKSMFFNENENSNQQLVGEKTKTETHKNANQVPELEVLSLLEQQLNQKDMQLQEK
                     DEQIKQMQKLLDHQQQLTLQANQQIEKLQEQLQLTYTEESSENKSTTLSEETESIEKQS
                     KTEKKWWQFWQ"
                     /name="DUF536 domain-containing protein"
     gene            complement(3359..4327)
                     /locus_tag="FLC01_RS15840"
                     /old_locus_tag="FLC01_16680"
     CDS             complement(3359..4327)
                     /locus_tag="FLC01_RS15840"
                     /old_locus_tag="FLC01_16680"
                     /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"
     Typing          complement(3364..4327)
                     /name="rep_cluster_1093"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="93.782"
                     /coverage="99.0"
                     /evalue="0.0"
ORIGIN
        1 gtacgtccta cggacgtatc gttcgtaatg tgaaagtacc tttaaaggta ctttctacaa
       61 aactcactaa agtgtttggc aagctctata tttgctagcc aaatacctac gtatttggtg
      121 caaataaccg cttgtcaaag gggcgcaagc tcccccttga atccccctca aaaaccacgc
      181 tccacaatac aaaaaaggct agcaaatgct agccactttt tgtaaagttt cgcttgtttc
      241 accttcggtg aaattattgt tttgtaatat caaacaacta ttcatcaatc agctttaaaa
      301 aattcaattg gtttagctgt cccttctgtc ccatcattcg ttgtcaaaat aaatacgagc
      361 ttttttggag aatccaaact aaaagtgtaa tctaattgtt ttttattaga gcgcagtgtt
      421 agtaaattat ttgttgcttt gtaaatgaaa acttgttcat ttatatttaa atttttatca
      481 atgatttgaa ttttatgatt gttctctttt actaagatgg tatattgttc tatatttttt
      541 gaagtattta aattagtgat tactagacgt tctgaatgat ctttagtttg ccaagttcct
      601 agaaaaggaa tcagatcagt cttttgtatt tcttgttttt ttgaacaact agttaagaaa
      661 agaactaaca ctagacccat aactaaagca atgggtttat ttaccaattt gtaatggtat
      721 tgtcccaagt aaaaccacct ccaggtacag gaattgtaac tggtcctgca tttgcactta
      781 ttacagttgg gtagttatac caaggattcc acacatagta agtttgataa ccaccttgat
      841 tgacccaccc aaataatgca agtgcatgac ggctgttact ataatttcca taaccagcag
      901 ttcccatata aatggcattt ccttttctta gttgtgtttg gacctctgaa aggtttagta
      961 ttcgtgctac ttttttagga taaacaccac agtaatttgc atattttatt atttgatctt
     1021 gattaagact ttttgattca atttgactat tccaatcatc aaggaaaaga ggagacctag
     1081 ataaattttc tttttgggtt tcaaaataac cacgcctttg tgttaaattt aagtggtata
     1141 cacctataat tatataatta aaatatacaa tatgcgataa caaatttttg ttatagttca
     1201 taaaatattg ttttgggaac ataatcgtta tttatcgagc tagttaacat aatgtacact
     1261 atgccaagta gcccctctac caatggatag agacgctcac tttgtgattt ttaattggtc
     1321 tagctaaaag caactttcta aagcttgatt tttcgcggtt atctatatct aattctttgt
     1381 gcatttttat ctgtcatttt tttaagactt gttatttttg agaggatttg atatgctttt
     1441 tttgtctttc tctagttctt cactttgtaa tatttttatg ttgatgaata ggataatctc
     1501 attttgggct gctcgtgaga gcagtctttt tttgtttcag ggtacgtcct attctttgga
     1561 tttccgcgct attaaataac cgatacttgg ggattggggt agcgccccaa aatacaaaaa
     1621 gaagaagttg cataagcgga tttttctttt ttttcgcaag ttggtaccaa cttgcaaatc
     1681 ttgctggaag actgatccct aaaaagaaat cgaggaattt ttttagggat cggtttcttt
     1741 ttttatcttt ttagaaagtt tgttgggtca aaatttccag aagtaaaggt ttgattggtt
     1801 tctttttgac gatttttggg ttgatttcgt cgggaaggat tgagttgatt ttcaattttt
     1861 tctttcactt cttgatacac tttagaattt gtaccgataa gaacaccagt atcttttaga
     1921 tataaatcag caaattctgc catgatttct gtcatgatag aaatttcttt tcccatggca
     1981 ttgagttttg cttggttact ggttgtggtt gtattggtat caggttcata actcatacat
     2041 aaaaaacgaa tggcttctga ataattgttg acgtctggat ttttttcgat gatggaatct
     2101 aaaacgtcaa cgtgactggg ataaagggtt acgtgttttt gaacagaagt ttttctcatg
     2161 ttatattcct ccgataagtg tttcaatgag ttggttgttt gtgtgaacat agtcattcag
     2221 tatgttcgta ttttctgttt gaatggcaat aaatttttcg agtaataaat cgaattgatc
     2281 ttttttgtaa ttcataagtt gacggtcaaa atcactttcg attagaactt ttagatattt
     2341 atttcgactc cattttttgc ccgttttggt tgtgagttcc tgacaacgtt tatctattct
     2401 tgcaataatt ttgggattga tatttcgaac taaaatgtcc atggaaattt tcctttcgta
     2461 tcagcgtata atttatgtat accatacaaa tatagtattt gtatagctat ttttcgccaa
     2521 aacactatac atagcctagc cacaatggca aaaaagtgat agcaaatttt tttctgagaa
     2581 acgtgatagg cacagcctat ctagcacctt tcgtaagaaa gtgataccac gtttccttat
     2641 gctctttcaa aattcagaaa aatcagctgt aaaacgagtg cagtccgagt aagattcaac
     2701 gaaaaaacgg ggattggggc gccaccaaaa tatcgcaaca tgggtccatg ttgctctgct
     2761 cgcaaaagca aaaagaagaa taaaaccagc aatttttatt aatttaaatt gctggtttta
     2821 ttgccagaat tgccaccatt ttttctccgt ctttgattgt ttttctatcg attctgtttc
     2881 ttcagaaaga gtcgttgatt tattttccga agattcttcc gtataagtca actgtagttg
     2941 ttcctgcagt ttctcgattt gttggttggc ttgcagggtg agttgttgtt ggtggtcgag
     3001 taatttttgc atttgtttta tttgctcgtc tttttcttgt agttgcatat ctttttgatt
     3061 taactgttgt tctaggagag aaaggacttc taattcggga acttggttgg cgtttttgtg
     3121 ggtttcggtt ttcgtttttt cgccaactag ttgttgattt gagttttcgt tttcgttaaa
     3181 aaacattgat tttatagcct tttgtccggt ttcattaatc acaaacttgt ttccgatttt
     3241 cgaaaaccaa agttttcgat tttcgtcaga aacttttttg ttaattgctg ttttactaac
     3301 tcctaattct tcagcaagtt ctttgattgt tttttctgtc ataaaatcta aaaacccctc
     3361 aatctttgaa taagttttga agattgtcta ataagtcttt ttttagttct gaaggaatat
     3421 cggaatttat ctctgatttt tgtgcattat tttctttatt ttgggtattt tgttctcttt
     3481 ctaacttttc taactgttgt aaaagttcca attttcgctt ttgttctttg attttttctt
     3541 gtaatgaagt aggtgctttt tcagattgaa cttgttggtt agctagttct aatgctttgt
     3601 tttgttcttc ttttgttggg gcatgtttgt taaagtcgtc tgattttttt atctcaggtt
     3661 taaatgtaaa ttgatagcca atgacaggct ttccccgtcc ttttccgtat ttctttttga
     3721 ttgttaaacc tttaaagatt gcggttagtt cttgtcgtat tggattgaac acacgttgat
     3781 caatcgtacc ttggttgtaa cttttaggaa tatcaagtaa ttcatgaaag tcttcttttg
     3841 aaaaataagc gaaacctttg gttctgtatt gttttagtaa tcgaaacatt gtttttgaat
     3901 aactgctttc taattcattg aattgttgga gagaatagcg cacccattct tcaagattat
     3961 taagtaaggg taaggctttt tcatgaactt gtatttcagc aaaaggaata tcagattttc
     4021 cgtcgatttt aaattgatta aataaaacaa aacgttcacg ttgcaaaccg tcagcacttc
     4081 ttctaccaaa acgtaaatcc attaatttgt catacgttgt ttctaaatca tctatgaatc
     4141 gaacatttgc agttgcttta taattgctta aatcttttaa ttgctcgaat gtaaattgta
     4201 cttttttatc acctacatca cgcattcttg atacgataga aaagaacaaa ttcatttcga
     4261 ctggtgtaaa ttttcgcaac ggaattgtat ttaattcatg atgatacttt acgatttcat
     4321 tagacatatt taaaatagct cctttcttac tcgcacaaga gatacacgtt atgaaataca
     4381 aaatgcctgt ttatctacat cttatattaa catcgtcgat gtactaattc aatgtacaaa
     4441 cagacaaaac gatgtagata aacagacaaa acgatgtaga taaacagaca aaacgatgta
     4501 gataaacaga caaaacgatg tagataaaag cgtcattccc ttgggagagt aaggatatag
     4561 ccgacggtaa agaggtttaa aaagaggttt aaaaagagat tataaaagag ggggacaaaa
     4621 tttcccgcct aaaaaaccac ttcttttttc tccaaacaga ttcgcgcatt tttctcaact
     4681 gggaatctta ctccctacag tcgcttaaaa aggtgtgatc gctctgctct cacattatac
     4741 tgcgcagtcg cttccggctc ctttgctaaa aatgttcata aggaactctt tgagaagcta
     4801 tgagccttcg tttgagacgt tttaagacag tcttagtata aatcccttat cttgttctta
     4861 aagcgcctta caggcggtca gggcaagccc taacaaccct aaagttgtct gaatgccctc
     4921 taaaattcga tttaagcact cttaaaccta ctcttatata tttatatact tagacgtttc
     4981 aaacgtctta aaacgcaaat tagagcttga taaagatatt tgctcgtgtg ccgacttttt
     5041 taaaagtcta ggcacacgcc atgacaaagc tgaaataaac tgcttcagct ttgtcatggc
     5101 ggattcgctc acttgaaaaa gtgttcattt cgctcgatta ttagcatata ttttttaact
     5161 ttttttgcta gccaaatttt gcattagttc gctcataaat cccacccttt ca
//
