LOCUS       NZ_CP041274             6173 bp    DNA     circular CON 20-APR-2024
DEFINITION  Enterococcus faecium strain VVEswe-S plasmid pVVEswe-S5, complete
            sequence.
ACCESSION   NZ_CP041274
VERSION     NZ_CP041274.1
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 6173)
  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 6173)
  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
            CP041274.1.
            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..6173
                     /organism="Enterococcus faecium"
                     /mol_type="genomic DNA"
                     /strain="VVEswe-S"
                     /isolation_source="feces"
                     /host="Homo sapiens"
                     /db_xref="taxon:1352"
                     /plasmid="pVVEswe-S5"
                     /geo_loc_name="Sweden:Halmstad"
                     /lat_lon="56.6744 N 12.8578 E"
                     /collection_date="2014"
                     /collected_by="Hospital of Halland"
     gene            1..945
                     /locus_tag="FLC01_RS15770"
                     /old_locus_tag="FLC01_16600"
     CDS             1..945
                     /locus_tag="FLC01_RS15770"
                     /old_locus_tag="FLC01_16600"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_002303559.1"
                     /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_002303559.1"
                     /translation="MANEIVKYHHELNTIPLRKFTPVEMNLFFSIVSRMREKGDKTVRF
                     TFDQLKDLSNYKATANVRFVEDLKATYEKILSLRFGRRSESGLSYDMFVMFTEFKINGD
                     VENPYVDIRIYEKALPLLNNLDEWVRYSLQQFNELQSGYAKTMFRLLKQYRTKGFAYFS
                     KEDFLELLDIPKSYKQPDIDKRVIKPIRQELTAIFKGLTIKKKYGKGRGKPVIGYQFTF
                     KPEIKKADDFNKHAPTKEDQNKALALADKQKEYEEPATTINEKIKQKKRELELLQQIKQ
                     LEKEKKALEKQTESALSEKEKKSLLSDLDNLFQ"
                     /name="replication initiation protein"
     gene            966..1499
                     /locus_tag="FLC01_RS15775"
                     /old_locus_tag="FLC01_16605"
     CDS             966..1499
                     /locus_tag="FLC01_RS15775"
                     /old_locus_tag="FLC01_16605"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_002292473.1"
                     /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_002363576.1"
                     /translation="MQPQETFTIKELSDLFKMSRQAISKHIQKLDSSMIAKNERGYKVV
                     LRSGVLQLARNLDNQRLLDKLHKHEQNNDKNAYIPNKNVVANKLLDQLREENEFLREQL
                     ALKEQNNSHIQKLLDQQQQLTLQANQQIEKLQEQLQLTYTEESSENSSTTLSEATETMD
                     EQTKNWKKWWQLWK"
                     /name="DUF536 domain-containing protein"
     gene            1514..1684
                     /locus_tag="FLC01_RS15780"
                     /old_locus_tag="FLC01_17115"
     CDS             1514..1684
                     /locus_tag="FLC01_RS15780"
                     /old_locus_tag="FLC01_17115"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_002322958.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_032491833.1"
                     /translation="MTKKHLLFGSILLGILSFSPMLLSVANKGNKKGELKLNPNYYNSQ
                     NEEVFVEKLDK"
                     /name="hypothetical protein"
     gene            2139..2363
                     /locus_tag="FLC01_RS15785"
                     /old_locus_tag="FLC01_16610"
     CDS             2139..2363
                     /locus_tag="FLC01_RS15785"
                     /old_locus_tag="FLC01_16610"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_002363584.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="class II bacteriocin"
                     /protein_id="WP_002363584.1"
                     /translation="MKKKVLKHCVILGILGTCLAGIGTGIKVDAATYYGNGLYCNKEKC
                     WVDWNQAKGEIGKIIVNGWVNHGPWAPRR"
                     /name="class II bacteriocin"
     gene            2383..2670
                     /locus_tag="FLC01_RS15790"
                     /old_locus_tag="FLC01_16615"
     CDS             2383..2670
                     /locus_tag="FLC01_RS15790"
                     /old_locus_tag="FLC01_16615"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_002363589.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="bacteriocin immunity protein"
                     /protein_id="WP_002363589.1"
                     /translation="MDFTKEEKLLNAISKVYNEATIDDYPDLKEKLFLYSKEISEGKSV
                     GEVSMKLSSFLGRYILKHKFGLPKSLIELQEIVSKESQVYRGWASIGIWS"
                     /name="bacteriocin immunity protein"
     gene            3120..3500
                     /locus_tag="FLC01_RS15795"
                     /old_locus_tag="FLC01_16625"
     CDS             3120..3500
                     /locus_tag="FLC01_RS15795"
                     /old_locus_tag="FLC01_16625"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_002348702.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MobC family plasmid mobilization relaxosome
                     protein"
                     /protein_id="WP_010782660.1"
                     /translation="MSEQNQYLASNHSKKYTYRSEPKQISFRVSESEFAKLKQSAEALQ
                     MSVPAFVKAKAQNARLVTPKVAPDIAQAIARDLAKAGGNINQIAKWCNTHQHDVDPGDA
                     QRLSENLKIMQKELQKIWQQLK"
                     /name="MobC family plasmid mobilization relaxosome protein"
     gene            3482..4396
                     /locus_tag="FLC01_RS15800"
                     /old_locus_tag="FLC01_16630"
     CDS             3482..4396
                     /locus_tag="FLC01_RS15800"
                     /old_locus_tag="FLC01_16630"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_002340563.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="relaxase/mobilization nuclease domain-containing
                     protein"
                     /protein_id="WP_010782659.1"
                     /translation="MATVKVSRTTSCSRAINYAEPRATVKTGINCDIDYAKSEMKQIRM
                     LYGKDDRVQAHLLIQSFRPGEITAEKANQLGAEYAKKIAPDHQIAIYTHTDKDHIHNHI
                     VINSVNLETGNKFQAHGQAFLNKCYDLNDEICLEHDLTITERGKKPEKRTMSEIKLKEK
                     NEPVWKDEIRFAIDQTMKNKKTRTYNQFCDSLKTFGIHCLNRGKNFTYELIHKKKKVRS
                     NKLGKDYEKETILHELDRRERAYNQQRTNELRRARASIRETAKEVRREQRTLTTEQPEI
                     RPTRRNHDQHVERGADYQQELSF"
                     /name="relaxase/mobilization nuclease domain-containing
                     protein"
     gene            4641..5330
                     /locus_tag="FLC01_RS15805"
                     /old_locus_tag="FLC01_16640"
     CDS             4641..5330
                     /locus_tag="FLC01_RS15805"
                     /old_locus_tag="FLC01_16640"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_002298772.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_002369882.1"
                     /translation="MAFYLPYLLIFASILGIIWLSYKAYQTRYSLKGSKIRFKRFLLPG
                     VIFTLSIVLSGLFGVLEGNKRISRSILLGDITQKYEAACDKKKKEQVLTQKMEEFTTCY
                     EEMNDIFVNQEKRLTDKNMEKLTRLYQNLPEKQQKEVQDNYERTKKDVQYFKDTQTEEA
                     CYNLFSDTIPFSTSEQERKERQQSVTYERYKALLQQATNIQNPTKKETALNYLKSVKEW
                     LDQQQQN"
                     /name="hypothetical protein"
     BGC             1..6173
                     /name="RiPP-like"
                     /gene="RiPP-like"
                     /tool="antismash"
     Typing          2..945
                     /name="rep_cluster_1197"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          3483..4393
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="93.421"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 atggctaatg agattgtaaa ataccaccat gaattaaata caattccttt aagaaaattt
       61 acaccggttg aaatgaattt gtttttttcc atcgtgtcta gaatgcgtga aaaaggggat
      121 aagacagttc gttttacgtt tgaccaacta aaagatttaa gtaactacaa agcaactgca
      181 aatgtacgat ttgtagaaga tttaaaagca acttatgaaa aaatcttatc tttacgcttt
      241 ggtcgtagaa gtgagtctgg gctttcttac gatatgtttg taatgtttac agaatttaaa
      301 atcaacgggg acgtagaaaa tccttacgta gatatacgaa tttacgaaaa agcactgcct
      361 ttgttaaata atttagacga gtgggtacgc tattctttac aacaattcaa cgagctacaa
      421 agtggctatg caaagactat gtttcgtctg ttaaagcaat acagaaccaa aggtttcgca
      481 tatttctcca aagaagactt tcttgaatta ttagatattc ctaaaagtta taagcaacct
      541 gatatagata aacgagttat aaaacctata cgtcaagaac taactgcaat cttcaaagga
      601 ctaacaatca aaaagaaata cggaaaagga cggggaaaac ctgttattgg ctatcaattt
      661 acgttcaaac ctgagatcaa aaaagcagac gactttaaca aacatgcacc aaccaaagaa
      721 gaccaaaata aagcattggc tttagctgat aaacaaaaag aatacgaaga acccgctaca
      781 acaattaacg aaaaaatcaa acagaagaaa cgagaacttg aactcctcca acaaatcaaa
      841 caactagaaa aagagaaaaa agctcttgaa aaacaaacag agtccgcact ttcggaaaaa
      901 gagaaaaaaa gtttattatc tgatttagat aatttattcc agtagcaacc taggaggcaa
      961 ccagtatgca accacaagaa acctttacaa taaaggaatt gtcagatctt tttaagatga
     1021 gtaggcaagc aatatcgaaa catatccaaa aattagattc ttccatgata gctaaaaatg
     1081 agcgtggtta taaggttgta ttgcgttctg gagtattgca acttgctcgc aacttagaca
     1141 atcaaaggtt gctagataag ttgcataaac atgaacaaaa caacgataaa aatgcttata
     1201 taccaaacaa aaacgtggtt gcaaacaagt tgctagatca gttgcgtgaa gaaaatgaat
     1261 ttttacgaga acaacttgcc ctcaaagagc aaaataattc tcatatacaa aaactactcg
     1321 accagcaaca acaactcacc ctgcaagcca accaacaaat cgaaaaactt caggagcaac
     1381 tgcagttgac ttatacggaa gagtcttcag agaatagttc aacgactctt tctgaagcaa
     1441 cagaaacaat ggacgaacaa acaaagaatt ggaaaaaatg gtggcagcta tggaaatgaa
     1501 gaaggaaata cttatgacaa aaaaacactt gctattcggt tctatcctac taggaatatt
     1561 aagctttagc ccaatgttat tatcagtggc caacaaagga aataaaaaag gggaactaaa
     1621 actcaatcct aattactaca acagtcaaaa tgaggaagta tttgtagaaa aacttgataa
     1681 ataagaaaag actgctcgta cgagcagtct ttctgaaaga gattatccta ttattaacct
     1741 tagaaaagaa taataaatga atatgagata tgtaaaaagc ataacaaaca caaacaaaaa
     1801 taacaagtat ttaaaaaatg accgatcaat attcacaaag aattagaaag aaacaaccgc
     1861 agaaaaccaa gccttaaaaa gagcttttaa cctagaccaa taaaaattca caaaatcagc
     1921 gcctggatcc cttggtacag gcgttacttg gtagtataca cattatgtct actagctgtt
     1981 taaataactg atcttataat tttatttaaa cgattatgaa ttcaaaacta ctttttatga
     2041 cgttaatcat tgttatataa taaaatgtta tataataaaa ttactaagat tatttaatat
     2101 aacaagcaat tttaaaaaaa cgaaaaggaa aaacaatcat gaaaaagaaa gtattaaaac
     2161 attgtgttat tctaggaata ttaggaactt gtctagctgg catcggtaca ggaataaaag
     2221 ttgatgcagc tacttactat ggaaatggtc tttattgtaa caaagaaaaa tgttgggtag
     2281 attggaatca agctaaagga gaaattggaa aaattattgt taatggttgg gttaatcatg
     2341 gtccatgggc acctagaagg tagtggtagg gaggttatta taatggattt tactaaagaa
     2401 gaaaaacttt taaatgcaat tagtaaagta tacaatgaag caactataga tgactatcct
     2461 gacttaaaag aaaagctctt tctttattct aaagaaatca gtgagggaaa aagtgttggt
     2521 gaagttagta tgaaattaag tagttttctt ggaagatata ttttaaaaca taaatttgga
     2581 ttacctaaat ctttaataga attacaagaa attgttagta aggaatctca agtatataga
     2641 ggatgggctt ctattggtat ttggagttaa ttctttggaa taaaatgaaa atgggactga
     2701 agaatcaatt ctgattcatc agtcccataa attatagagc cgaaaaatta tcatatttat
     2761 agatttatta atagtaaatg gcataagaat ctttgaacaa cgaaaaaaat gtagctctac
     2821 ctaattattg atttgcaaca atttcaccga aggtgaaaca agcgaaactt tacaaaaagt
     2881 ggctagcatt tgctagtctt ttttgtattg tggagagtgg gggggagggg gattcaaggg
     2941 ggagcttgcg cccctttgac aagcggttat ttgcaccaaa tacgtaggta tttggctagc
     3001 aaatatagag cttgccaagc cctttagtga gctttagtga gctttactta ttgtaccttt
     3061 ttaggtacaa tggtattgcg aacgatacgt ccgtaggacg tactgaaagg gtgggactta
     3121 tgagcgaaca aaatcaatat ttggctagca atcattctaa aaaatatacc tatcgatccg
     3181 agccaaaaca aatcagtttt cgagtgagcg aatccgaatt tgcaaagctg aagcagtcag
     3241 ctgaagcttt gcaaatgagt gtgccggctt tcgtgaaagc caaggcacaa aacgcgcgtc
     3301 tggtgacacc gaaagtggcg ccagacattg ctcaggcaat cgcgcgcgat ttagccaaag
     3361 ctggcgggaa tatcaatcaa attgccaagt ggtgcaacac acaccaacac gacgttgatc
     3421 ctggcgacgc ccaacgctta tccgaaaacc taaaaatcat gcaaaaggag ctacaaaaga
     3481 tatggcaaca gttaaagtaa gccgaaccac ttcttgtagc cgagcgatca attacgccga
     3541 accacgagca accgtcaaaa cagggataaa ctgtgacatt gattatgcca aaagcgaaat
     3601 gaaacaaatt cgcatgctgt atggaaaaga cgatcgtgta caagcacact tattgatcca
     3661 gtcttttcga ccaggagaaa ttaccgctga aaaagccaat caactagggg cagagtatgc
     3721 gaaaaaaata gcccctgacc accaaatcgc gatttacaca catacagaca aagaccatat
     3781 tcataaccac attgtcatta actccgtcaa tctggaaact gggaacaaat ttcaagccca
     3841 tggtcaagca tttttaaaca aatgttatga cctaaatgac gagatttgtc ttgaacatga
     3901 cttaacaatc actgaacgag ggaagaaacc cgaaaaacga accatgtctg aaatcaaatt
     3961 aaaagaaaaa aatgaacctg tttggaaaga cgaaattcgg tttgcgattg atcaaacaat
     4021 gaaaaacaaa aaaactcgaa cgtataacca attttgtgat tctcttaaaa cattcggcat
     4081 tcattgcttg aatcgtggga aaaattttac ttacgaattg atccacaaaa agaaaaaagt
     4141 acgatccaac aaactaggaa aggattacga aaaggagacg attttacatg agctggacag
     4201 acgagaacga gcctacaatc aacaacgaac caacgagcta cgaagagctc gagctagcat
     4261 tcgcgaaact gcaaaagaag tacgaagaga acaacgaact cttacgactg aacaaccgga
     4321 aattagaccg actcgaagaa accatgacca acacgttgaa agaggagcag actaccaaca
     4381 agaattatcg ttctaaaacg ttacaagaca tagaaaatga aataaagaaa caacgtgctt
     4441 ttcttgcacc ttataccaaa gaaagaatac aaactacaat tgattcacaa gtcaaaaaat
     4501 tccaccatgc gctattaaac cagcgaaata aagaacagaa aaaagtaatt atgcagcgat
     4561 caatggatat tcttgccccc ttatgttgct taatcatgac actgttagcc ttttggctgg
     4621 tatggggaga ataaatagaa atggcattct atttacccta tctactcatt tttgccagta
     4681 ttttaggaat tatttggctt agctataagg cttatcaaac aagatattca ttaaaaggct
     4741 ctaaaattcg atttaagagg tttttattgc caggggttat atttacatta tcaatcgttt
     4801 taagtggttt attcggcgtt ttagagggaa ataaacgtat ttcaagaagt attttattag
     4861 gggatatcac tcaaaagtat gaagcagcat gtgataaaaa gaaaaaggag caagtgttaa
     4921 cacaaaaaat ggaagagttt accacttgtt atgaggaaat gaacgatatt tttgtgaatc
     4981 aagaaaaacg tttgacggat aaaaacatgg aaaaactcac tcgtctttat caaaacttgc
     5041 cagaaaaaca gcaaaaagag gttcaagaca actatgagcg aaccaaaaaa gacgtgcaat
     5101 attttaaaga tacgcagaca gaagaagctt gttataattt attcagtgat acaatccctt
     5161 tttcaactag tgaacaggaa cgaaaagaac ggcaacaatc agttacctac gaacgttata
     5221 aagcactgct tcagcaagca acgaacatac aaaatccaac gaaaaaagaa acggcattaa
     5281 attatctaaa aagtgtcaag gaatggttag atcagcaaca gcaaaattga atttgatcgg
     5341 caatcatgtt aaactaaaca tgcaaatgat caaacattag atacacgaaa gccccagaga
     5401 ggtcggattc tctggggctt tttttcaggt tgatgtcgcc tttattgatt ttacttcttg
     5461 tttcggttat tcaaccaata actgaataaa gagacacaaa cttctataag aagggggcaa
     5521 atgaacaatt caaacattag atacacctcc ttccagtcgc aagactgtcg gataggcgac
     5581 aagttattat atcttaaaaa attaaacttg tgtggtgttt ttaagtatcg cttattttag
     5641 ggttgttagg gcttgccctg accgcctgta aggcgcttta aagctagata aggattttta
     5701 tccaagactg tcttaaaacg gcttagataa gcattcagaa ccgctcaaag gcctctttac
     5761 caacatgttt ttagcaaagg agcctttagg cgactgcgca gtacaatgtg agagcgtagc
     5821 gatcacacct ttttggcgac cgtaggaagc aaggttttgg attggcagtt ttgaaaaatg
     5881 cgcgaacctg tttaaagaaa aaagaagtgg tttttaggcg ggaaaattag cccccctctt
     5941 tttatatctc tttttaaacc tctttttaaa cctctttacc gtaagctgtg tccttactct
     6001 accaatggat acagaatgtt atgaaggaca ttttgtctgt ttatgaagga cattttgtct
     6061 gtttatgaag gacattttgt ctgtttatga aggacatttt gtctgtttga acgtcaaata
     6121 tgaatgtctt gacatttaaa aaatgtcatt cataattgga ttgaggtgat tat
//
