LOCUS       NZ_CP083925             4979 bp    DNA     circular CON 05-NOV-2023
DEFINITION  Enterococcus faecium isolate V1164 plasmid pV1164-5, complete
            sequence.
ACCESSION   NZ_CP083925
VERSION     NZ_CP083925.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMEA5367917
            Assembly: GCF_020162175.1
KEYWORDS    RefSeq.
SOURCE      Enterococcus faecium
  ORGANISM  Enterococcus faecium
            Bacteria; Bacillota; Bacilli; Lactobacillales; Enterococcaceae;
            Enterococcus.
REFERENCE   1  (bases 1 to 4979)
  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  JOURNAL   Unpublished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 4979)
  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                     :: 03-JAN-2019
            Assembly Method                   :: Unicycler v. 4.0.7
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 254.19410228420895x
            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 01:58:33
            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)                     :: 2,998
            CDSs (total)                      :: 2,907
            Genes (coding)                    :: 2,780
            CDSs (with protein)               :: 2,780
            Genes (RNA)                       :: 91
            rRNAs                             :: 6, 6, 6 (5S, 16S, 23S)
            complete rRNAs                    :: 6, 6, 6 (5S, 16S, 23S)
            tRNAs                             :: 69
            ncRNAs                            :: 4
            Pseudo Genes (total)              :: 127
            CDSs (without protein)            :: 127
            Pseudo Genes (ambiguous residues) :: 0 of 127
            Pseudo Genes (frameshifted)       :: 45 of 127
            Pseudo Genes (incomplete)         :: 76 of 127
            Pseudo Genes (internal stop)      :: 35 of 127
            Pseudo Genes (multiple problems)  :: 26 of 127
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP083925.1.
            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..4979
                     /organism="Enterococcus faecium"
                     /mol_type="genomic DNA"
                     /isolate="V1164"
                     /isolation_source="Hospitalized patient"
                     /host="Homo sapiens"
                     /db_xref="taxon:1352"
                     /plasmid="pV1164-5"
                     /geo_loc_name="Denmark"
                     /collection_date="2015"
     gene            complement(join(4412..4979,1..449))
                     /gene="tsaD"
                     /locus_tag="LCG90_RS14840"
                     /old_locus_tag="LCG90_14865"
     CDS             complement(join(4412..4979,1..449))
                     /gene="tsaD"
                     /locus_tag="LCG90_RS14840"
                     /old_locus_tag="LCG90_14865"
                     /EC_number="2.3.1.234"
                     /inference="COORDINATES: ab initio prediction:GeneMarkS-2+"
                     /GO_process="GO:0006400 - tRNA modification [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GeneMarkS-2+."
                     /codon_start=1
                     /transl_table=11
                     /product="tRNA
                     (adenosine(37)-N6)-threonylcarbamoyltransferase complex
                     transferase subunit TsaD"
                     /protein_id="WP_002301319.1"
                     /translation="MNEELILAIESSCDETSVAVVRNGTEILSNIVASQINSHKRFGGV
                     VPEVASRHHVEQITLCLEDALVEAGVSAEDLSAVAVTYGPGLVGSLLIGISAAKAFAWA
                     HQLPLIPVNHMAGHIYAARLVKPFQFPLMALLVSGGHTELVYMQEDGSYEIIGETRDDA
                     AGEAYDKVGRVLGLSYPSGKEIDQLAHQGKDNYHFPRAMIHEDNYDFSFSGLKSAFINL
                     VHNAQQRGEDLDKNDLAASFQASVIDVLITKTLRACQNYPVKQLIIAGGVAANQGLREG
                     LQDALATKLPEVELVIPPLRLCGDNAAMIGAAAHVEMQKRNFASYQLNADPSLVLSE"
                     /name="tsaD"
     gene            complement(446..910)
                     /gene="rimI"
                     /locus_tag="LCG90_RS14845"
                     /old_locus_tag="LCG90_14870"
     CDS             complement(446..910)
                     /gene="rimI"
                     /locus_tag="LCG90_RS14845"
                     /old_locus_tag="LCG90_14870"
                     /EC_number="2.3.1.266"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_002335773.1"
                     /GO_function="GO:0008999 -
                     peptide-alanine-alpha-N-acetyltransferase activity
                     [Evidence IEA]"
                     /GO_process="GO:0036211 - protein modification process
                     [Evidence IEA]; GO:0042254 - ribosome biogenesis [Evidence
                     IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="ribosomal protein S18-alanine
                     N-acetyltransferase"
                     /protein_id="WP_002288445.1"
                     /translation="MICRKKDFDEAYLAECVWMISENAYPHGSPWTKMQFLADIQQPHS
                     DYLLLAEDNQICGFIGYSKVIDEVEITNIAVAVSEQGKGHARHLLQLLITEQIKDSLHV
                     FLEVRLSNEAARKLYESEKFRILGKRKSYYRNPTEDAIIMSRKLKTETMK"
                     /name="rimI"
     gene            complement(917..1459)
                     /gene="rimI"
                     /locus_tag="LCG90_RS14850"
                     /old_locus_tag="LCG90_14875"
     CDS             complement(917..1459)
                     /gene="rimI"
                     /locus_tag="LCG90_RS14850"
                     /old_locus_tag="LCG90_14875"
                     /EC_number="2.3.1.266"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_002348676.1"
                     /GO_function="GO:0008999 -
                     peptide-alanine-alpha-N-acetyltransferase activity
                     [Evidence IEA]"
                     /GO_process="GO:0036211 - protein modification process
                     [Evidence IEA]; GO:0042254 - ribosome biogenesis [Evidence
                     IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="ribosomal protein S18-alanine
                     N-acetyltransferase"
                     /protein_id="WP_002288446.1"
                     /translation="MLKKFRAYARSFFQDKMIYTEKTVEQIDRRYVLRELTTEDIKELL
                     DVEREVYNGELPWTKSAFISELKSPLPHLYLGIFDNGRMIGFIGSRAFGLDCHITNIAV
                     RPAYQRKRIGSLLIDEIENFAIMNRCETMSLEVRMSNQDAQRLYRKLGFQATTIKKRYY
                     TETKEDALDMIKLLENE"
                     /name="rimI"
     gene            complement(1443..2165)
                     /gene="tsaB"
                     /locus_tag="LCG90_RS14855"
                     /old_locus_tag="LCG90_14880"
     CDS             complement(1443..2165)
                     /gene="tsaB"
                     /locus_tag="LCG90_RS14855"
                     /old_locus_tag="LCG90_14880"
                     /EC_number="2.3.1.234"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_002326913.1"
                     /GO_function="GO:0003725 - double-stranded RNA binding
                     [Evidence IEA]"
                     /GO_process="GO:0006400 - tRNA modification [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="tRNA
                     (adenosine(37)-N6)-threonylcarbamoyltransferase complex
                     dimerization subunit type 1 TsaB"
                     /protein_id="WP_002343909.1"
                     /translation="MITLGIDTANQTLAIGVVEDEQILGQIQTNIKRNHSVTLMPAIDQ
                     LFADLQISPKDIDRIAVSDGPGSYTGLRIGVTTAKTIAYTLDKELVGVSSLKTIAANCI
                     GVDNIIVPMFDARRKNVYAGAYRWKENRLETVLEDVHISASDLFTQLQKLNEAIYFVGS
                     DCHKFFSEIKEILPSAMINTVPAWDIPSGVTVAQLGALVEPVAEKQAFLPRYLKRVEAE
                     EKWLETHTPGDESYVEKI"
                     /name="tsaB"
     gene            2453..3748
                     /locus_tag="LCG90_RS14860"
                     /old_locus_tag="LCG90_14885"
     CDS             2453..3748
                     /locus_tag="LCG90_RS14860"
                     /old_locus_tag="LCG90_14885"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_002297185.1"
                     /GO_function="GO:0004803 - transposase activity [Evidence
                     IEA]"
                     /GO_process="GO:0006313 - DNA transposition [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="ISL3-like element ISEfa5 family transposase"
                     /protein_id="WP_002297185.1"
                     /translation="MNDSIKKMLRLIEKDLMITEVSYETFQKKKTLIVDAVFSPAPHTC
                     RNCGSTVVDGNGKVIVVKNGKKETIVRFEQYNHMPLVMRLKKQRYTCKNCRTHWTAQSY
                     FVQPRHSIANHVRYKIASLLTEKVSLSFIAKNCQVSLTTVIRTLKEFKSYLPKQSKRIL
                     PRVLMVDEFRSHASIEDKMSFICADGETGQLIDVLPTRKLPRLTSYFLGCANPEEVKFL
                     VTDMNAAYFQLTKRILPNAKVVIDRFHIIKHMNQAFNELRIREMNELRKVGQKSQAEKL
                     KKNWRFLLKNRANINHYEYKTWKSFRAPKYPFLTEAMMIDRLLGFSTSLKEAYPYFHEL
                     VEAFRDKDPDLFFSLLAELPETLDDGFREKLQNLLTYEEGITNAMIYPYTNGKIEAKNT
                     HIKTMKRVSYGFKSFENMRIRIFLINQLIKVR"
                     /name="ISL3-like element ISEfa5 family transposase"
ORIGIN
        1 tcttcttgca tatagactaa ttctgtatgt cctccgctaa caagaagtgc catcaatgga
       61 aactggaatg gtttaaccag acgggctgca tagatatgcc ctgccatatg gtttacagga
      121 ataagcggca attggtgtgc ccaagcaaaa gccttagctg cagaaatacc aatcagcaac
      181 gagccgacaa gtcctggtcc ataagtgaca gcgactgccg ataaatcttc tgccgacaca
      241 ccagcttcta ccagtgcatc ttccaagcat aaggtgattt gttctacgtg atggcggcta
      301 gctacttcag gtactacgcc accaaaacgt ttatgactgt ttatttgaga agcaacgatg
      361 ttagataaga tctctgttcc atttctaacg accgctacac tcgtttcatc acaacttgat
      421 tcaatcgcca gaatcaattc ttcattcatt tcatcgtctc cgtttttaac tttctgctca
      481 taatgatcgc atcttccgtc ggattgcgat aatatgattt ccgtttacct aatatacgaa
      541 acttttctga ttcataaagt tttcttgctg cttcattaga tagacgtact tctaaaaaaa
      601 catgcagcga atcttttatt tgttccgtaa tcagtaattg taacaaatgc cgtgcatgcc
      661 cttttccttg ttctgaaact gcaacagcaa tatttgtgat ctcgacttca tctattactt
      721 tcgagtatcc aataaagcca cagatctggt tatcttcagc taaaagcaga taatcagagt
      781 gaggctgttg gatgtctgcc aaaaactgca ttttcgtcca aggtgaacca tgtggataag
      841 cattttcgct aatcatccat acgcattctg ccaagtacgc ttcatcaaaa tctttttttc
      901 tgcaaatcaa ctaatctcac tcattttcta aaagttttat catatccaac gcatcttctt
      961 ttgtttcagt gtaatatctt tttttgatcg ttgttgcttg aaaccccaat ttccgataaa
     1021 gtctttgtgc atcttgatta ctcatacgca cttctaatga catcgtctca cagcgattca
     1081 ttatagcaaa gttctcgatt tcgtcaataa gcagcgaacc gattcgttta cgctgatatg
     1141 ccggtcgaac ggcaatattc gtgatatggc aatctaaacc gaacgctctt gaaccgataa
     1201 aaccaatcat tcttccatta tcaaagatac ctagatatag atgaggaagc ggtgacttca
     1261 attctgatat aaaggcactt tttgtccatg gcaattcgcc attatagact tctcgttcga
     1321 catccagcag ctctttgata tcttctgtag tcaattctct tagtacgtaa cgacgatcga
     1381 tttgttcgac tgttttttct gtataaatca ttttatcttg aaaaaagctt ctggcatacg
     1441 ctctaaattt tttcaacata actttcgtct ccaggtgtgt gcgtctccaa ccatttttct
     1501 tctgcttcta ctcgttttaa atagcgagga agaaaagctt gtttctctgc aactggttca
     1561 actaaagcac ctaattgagc cacagttaca ccacttggaa tatcccatgc tggaactgta
     1621 ttaatcatcg cactaggcaa tatttccttt atttcagaga agaatttgtg acaatcactc
     1681 ccgacgaaat aaatagcttc attcagcttt tgtagttgtg tgaacaaatc agaagcagaa
     1741 atatgtacat cttcaagtac agtttctaat ctattttctt tccagcggta tgccccagcg
     1801 tatacatttt ttcttcgagc atcaaacatg ggcacaataa tattatccac accgatgcaa
     1861 ttagccgcga tggttttcag actagatact cctactagct ctttatctaa tgtataagca
     1921 atcgtttttg ctgtcgttac acctatacga agccctgtat aagaaccggg accatcagaa
     1981 accgcgattc ggtcaatgtc ttttggactt atttgaagat ctgcaaacaa ttggtcgatt
     2041 gcaggcatca gtgttacact gtggttgcgt ttgatatttg tttgtatttg tccaagaatt
     2101 tgttcgtctt ctaccacacc gatcgccaaa gtttggtttg cagtatctat tcctaatgta
     2161 atcatatatt tgatcctttc tgctatgaca ttctcgcctt ccattgtagc atactttttt
     2221 attctgagga tgaaaatacc aaaggcaaaa ctagtacaat aatacatgat tatctgctgg
     2281 cgggcaaatt ttgccccttc ctgaaacaca aaaaagggct ctataattta tgggactgat
     2341 gaatcagaat tgattcttca gccccatttt tattttaggt attaaaaaac atatcgttct
     2401 ctagtatgat taaatcacga caaaataaac aactgagagg acgatatgct atatgaatga
     2461 ttctatcaaa aaaatgctgc gattaataga gaaagatttg atgattacag aggtctctta
     2521 cgagaccttt cagaagaaaa agacgttgat cgtcgatgct gttttctcac ctgctcccca
     2581 tacctgtaga aattgtggtt ctactgtggt agatggaaac gggaaagtaa ttgtagtgaa
     2641 aaatgggaag aaggaaacga ttgtccgctt tgaacaatac aatcacatgc ctttggttat
     2701 gcgcttaaaa aagcagcgct atacctgtaa aaactgtcga acccattgga cggctcaaag
     2761 ttattttgtt caacccagac attcaatcgc gaatcatgtc agatataaaa ttgcttcttt
     2821 actgactgaa aaagtatctt tatcttttat tgcgaaaaat tgtcaggtat ctttgaccac
     2881 cgttattcgt acgttgaaag agtttaaaag ctacttacca aagcaatcta agaggattct
     2941 ccccagagta ttgatggttg atgaatttcg ttcgcacgct tccatagaag ataaaatgag
     3001 ctttatttgc gcagatggcg aaacaggaca attaattgat gtcttgccta cgcgtaaatt
     3061 gcctcgatta acaagctatt tcttaggctg cgctaatcct gaagaagtaa aatttttagt
     3121 cacagacatg aacgccgcct acttccagct taccaaacgt attctgccaa atgcgaaagt
     3181 agtgattgat cggtttcata ttatcaaaca catgaatcaa gcctttaatg agttgcgtat
     3241 ccgtgaaatg aatgaacttc gtaaagtagg acagaaaagt caggcagaaa aactgaaaaa
     3301 gaactggcgc tttttgctaa aaaatcgtgc aaacatcaac cattatgaat acaaaacatg
     3361 gaaaagtttt cgagcaccaa aatacccatt tcttacggaa gcgatgatga ttgatcgatt
     3421 gcttggcttt tctacgtccc tgaaggaggc gtatccctat tttcatgaat tagttgaagc
     3481 ctttcgagac aaagaccctg acttattttt ctccttattg gcagaacttc ccgaaacgtt
     3541 agatgacggc tttcgggaaa agctccaaaa ccttctgacc tatgaagaag gcatcaccaa
     3601 cgcgatgatc tatccttaca ccaatggaaa aatagaagcg aagaataccc atataaagac
     3661 aatgaaacga gtatcctacg gatttaaatc atttgagaac atgagaatta gaatcttttt
     3721 gatcaatcaa ttaatcaaag taagataaca aaaaatctga gccagaatga ggttcattct
     3781 gacccagatt tgattttgta caacccatca gtccttattg acaaagagcc ataaatatca
     3841 gggtcactgc ttattttcct ccctaaaact tctgaaagat ccggcagttt tagatcactg
     3901 gacaagactc aaagattttc tatgtgtgtt tcagttatgt aatattcact gtttgcaaaa
     3961 aatactgtta gattaactag atgaagcgtc ttgtcctcat ccgatctaga ttattcgata
     4021 ttcctcgaca ataaacgatt actcagtgag ggcaatcaga ggaacggata atgataaata
     4081 agctgtaaaa aatagcaaaa taacaataat gattaaaagt atgtaaaaaa tagggctttg
     4141 acaaaaacgt gtcacagccc tatttcgatt aaacggtgtg tacctgtcaa ctcttcggtc
     4201 acaagtcata atgttcataa acatgaggag ctgttttttg aaattgttcc ttgtgaatca
     4261 gagttaaacg acaggcttac gaactcttga ttaaacggcg ttcaaaagct tgcatacgcg
     4321 gtaataagaa cagccaggtc aaaaacatga gaagccgttt ttcctgggct gttcttatta
     4381 cttgatgcag ggcagctttt tcacaacctc tttattcaga taaaaccaag cttggatcag
     4441 cattcaactg atagctagca aaatttcttt tttgcatttc cacatgtgct gctgctccaa
     4501 tcattgcagc attatctcca caaagtcgaa gagggggaat cactagttct acctcaggga
     4561 gtttagttgc caaagcatcc tgcaatcctt cacgcaaccc ttgattggcc gctacacctc
     4621 cagctataat cagttgcttg actggataat tttgacaagc tcgaagtgtt ttagtaatca
     4681 atacatcgat cacacttgct tgaaagctag ctgctaaatc atttttgtct agatcttctc
     4741 cacgctgttg tgcattatgc accaaattga taaatgcact ttttaatccg ctaaaactga
     4801 aatcataatt atcttcatgg atcatcgctc gcggaaaatg gtaattatct tttccctgat
     4861 gagctagctg atcgatttct tttccgcttg ggtaagaaag acctaatact cttccaactt
     4921 tgtcataagc ttctcctgct gcgtcatctc ttgtctcccc aatgatttca tatgatcca
//
