LOCUS       NZ_CP066597             6263 bp    DNA     circular CON 20-FEB-2024
DEFINITION  Enterococcus faecium strain Dallas 107_1 plasmid p107_1_6.2kb,
            complete sequence.
ACCESSION   NZ_CP066597
VERSION     NZ_CP066597.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN17038094
            Assembly: GCF_016415325.1
KEYWORDS    RefSeq.
SOURCE      Enterococcus faecium
  ORGANISM  Enterococcus faecium
            Bacteria; Bacillota; Bacilli; Lactobacillales; Enterococcaceae;
            Enterococcus.
REFERENCE   1  (bases 1 to 6263)
  AUTHORS   Islam,M.J. and Palmer,K.
  TITLE     Molecular characterization of VREfm isolates from Dallas, Texas
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 6263)
  AUTHORS   Islam,M.J. and Palmer,K.
  TITLE     Direct Submission
  JOURNAL   Submitted (21-DEC-2020) Biological Sciences, University of Texas at
            Dallas, 1520 Richardson Dr Apt 1418, Richardson, TX 75080, USA
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Date                     :: 2019
            Assembly Method                   :: Unicycler v. 0.4.7
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 158.0x
            Sequencing Technology :: Illumina NextSeq; Oxford Nanopore MinION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 02/20/2024 02:50:02
            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)                     :: 3,125
            CDSs (total)                      :: 3,034
            Genes (coding)                    :: 2,918
            CDSs (with protein)               :: 2,918
            Genes (RNA)                       :: 91
            rRNAs                             :: 6, 5, 6 (5S, 16S, 23S)
            complete rRNAs                    :: 6, 5, 6 (5S, 16S, 23S)
            tRNAs                             :: 70
            ncRNAs                            :: 4
            Pseudo Genes (total)              :: 116
            CDSs (without protein)            :: 116
            Pseudo Genes (ambiguous residues) :: 0 of 116
            Pseudo Genes (frameshifted)       :: 43 of 116
            Pseudo Genes (incomplete)         :: 66 of 116
            Pseudo Genes (internal stop)      :: 30 of 116
            Pseudo Genes (multiple problems)  :: 19 of 116
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP066597.1.
            Bacteria and source DNA available from Dr. Kelli Palmer, UTDallas.
            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..6263
                     /organism="Enterococcus faecium"
                     /mol_type="genomic DNA"
                     /strain="Dallas 107_1"
                     /isolation_source="rectal swab"
                     /host="Homo sapiens"
                     /db_xref="taxon:1352"
                     /plasmid="p107_1_6.2kb"
                     /geo_loc_name="USA: Dallas"
                     /collection_date="2015"
     gene            1..945
                     /locus_tag="JCQ02_RS15480"
                     /old_locus_tag="JCQ02_15480"
     CDS             1..945
                     /locus_tag="JCQ02_RS15480"
                     /old_locus_tag="JCQ02_15480"
                     /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="JCQ02_RS15485"
                     /old_locus_tag="JCQ02_15485"
     CDS             966..1499
                     /locus_tag="JCQ02_RS15485"
                     /old_locus_tag="JCQ02_15485"
                     /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_196921171.1"
                     /translation="MQPQETFTIKELSELFKMSRQAISKHIQKLDSSMIAKNERGYKVV
                     LRSGVLQLARNLDNQRLLDKLHKHEQNNDKNAYIPNKNVVANKLLDQLREENEFLREQL
                     ALKEQNNSHIQKLLDQQQQLTLQANQQIEKLQEQLQLTYTEESSENSSTTLSEATETMD
                     EQTKNWKKWWQLWK"
                     /name="DUF536 domain-containing protein"
     gene            1514..1684
                     /locus_tag="JCQ02_RS15490"
                     /old_locus_tag="JCQ02_15490"
     CDS             1514..1684
                     /locus_tag="JCQ02_RS15490"
                     /old_locus_tag="JCQ02_15490"
                     /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            2140..2673
                     /locus_tag="JCQ02_RS15495"
                     /old_locus_tag="JCQ02_15495"
     CDS             2140..2673
                     /locus_tag="JCQ02_RS15495"
                     /old_locus_tag="JCQ02_15495"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_002334266.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_002334266.1"
                     /translation="MKKFTLGVALLTIGAVVLPSTTIVYASENSQVVSLNENNATENVV
                     IEYTEDGMVVTKYEDGYSAEDFANSSDIMTRAAVARWGKKEYTNIAVTTGVAANAINAA
                     FWAGGKASTSMFGIPGWAIGALLTGASWTKKGASPGNAVAKEWDKNGNGWIGFYYQRGY
                     DAAGRVVATRYSTL"
                     /name="hypothetical protein"
     gene            2685..2888
                     /locus_tag="JCQ02_RS15500"
                     /old_locus_tag="JCQ02_15500"
     CDS             2685..2888
                     /locus_tag="JCQ02_RS15500"
                     /old_locus_tag="JCQ02_15500"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_002307460.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_002321382.1"
                     /translation="MFLISKSLKSLKTFTKKNPQIATIRIFIFAIAVAIIVNMLSGGQL
                     YKSGLFLVLILVVLDIIKSKKK"
                     /name="hypothetical protein"
     gene            3210..3590
                     /locus_tag="JCQ02_RS15505"
                     /old_locus_tag="JCQ02_15505"
     CDS             3210..3590
                     /locus_tag="JCQ02_RS15505"
                     /old_locus_tag="JCQ02_15505"
                     /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_197669149.1"
                     /translation="MSEQHQNLASDHSKKYTYRSEPKQISFRVSESEFAKLKQSAEALQ
                     MSVPAFVKAKAQNARLVTPKVAPDIAQAIARDLAKAGGNINQIAKWCNTHQHDVDPGDA
                     QRLSENLKIMQKELQKIWQQLK"
                     /name="MobC family plasmid mobilization relaxosome protein"
     gene            3572..4486
                     /locus_tag="JCQ02_RS15510"
                     /old_locus_tag="JCQ02_15510"
     CDS             3572..4486
                     /locus_tag="JCQ02_RS15510"
                     /old_locus_tag="JCQ02_15510"
                     /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            4731..5420
                     /locus_tag="JCQ02_RS15520"
                     /old_locus_tag="JCQ02_15520"
     CDS             4731..5420
                     /locus_tag="JCQ02_RS15520"
                     /old_locus_tag="JCQ02_15520"
                     /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"
     Typing          2..945
                     /name="rep_cluster_1197"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          3573..4483
                     /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 gtcagaactt 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 gtagtatgta cattatgtca acaagaattt
     1981 aatataacat attttcctaa tgcattctaa ctataccaca ttatcaaaaa tataaattat
     2041 ctttactaaa taaaatattg acaagcctat accttttgtt ttatgatttt cacaaagaaa
     2101 acgttttcta tatatttttc tgtatcagga ggaaattcta tgaaaaaatt tactttaggg
     2161 gtagctttgt taactattgg ggcagttgtt ttaccgtcaa ctactatagt ttatgcttca
     2221 gaaaattccc aagtggtatc attaaacgaa aacaatgcta ctgaaaatgt agttattgag
     2281 tacactgaag atggtatggt cgtaactaaa tatgaggatg gttatagtgc ggaagatttt
     2341 gcaaattctt cagatatcat gacaagagct gcagttgcaa gatggggcaa aaaggaatat
     2401 acaaatattg ctgtaaccac tggagtagct gctaatgcta ttaatgctgc cttttgggca
     2461 ggagggaaag ctagcacttc tatgtttggt atcccaggtt gggcaattgg tgctttgtta
     2521 acaggtgcaa gttggactaa aaaaggtgct tctccaggga atgcagttgc aaaagaatgg
     2581 gacaaaaatg gtaatggctg gattggattt tattaccaaa ggggatatga tgcagctgga
     2641 agagttgtag ctactagata ttcaacgtta taagttaagg agtgatgttt ttgatatcta
     2701 aatcattaaa atcattaaaa acatttacta aaaagaatcc gcaaatagct actattcgta
     2761 tttttatatt tgctatagct gttgctataa ttgttaatat gctaagcgga gggcaattat
     2821 acaaatctgg tttattttta gtgttaatct tagttgtctt agacataata aagtctaaaa
     2881 aaaaataaat cgatacattt tagaagaata gggttgtttg aatattacaa agcaacaatt
     2941 tcaccttcgg tgaaataagc gaaactttac aaaaagtggc tagcaaatgc tagccttttt
     3001 ttgtattgtg gagcgtggat tttgaggggg attcaagggg gagcttgcgc tcctttgaca
     3061 agcggttatt tgcaccaaat acggaggtat ttggctagca aatatagagc ttgccaaacc
     3121 cttttagtga gctttactca ttgtaccttt ttaggtacaa tggtattgcg aacgatacgt
     3181 ccgtaggacg tactgaaagg gtgggactta tgagcgaaca acatcaaaat ttggctagcg
     3241 atcattctaa aaaatatacc tatcgatccg agccaaaaca aatcagtttt cgagtgagcg
     3301 aatccgaatt tgcaaagctg aagcagtcag ctgaagcttt gcaaatgagt gtgccggctt
     3361 tcgtgaaagc caaggcacaa aacgcgcgtc tggtgacacc gaaagtggcg ccagacattg
     3421 ctcaggcaat cgcgcgcgat ttagccaaag ctggcgggaa tatcaatcaa attgccaagt
     3481 ggtgcaacac acaccaacac gacgttgatc ctggcgacgc ccaacgctta tccgaaaacc
     3541 taaaaatcat gcaaaaggag ctacaaaaga tatggcaaca gttaaagtaa gccgaaccac
     3601 ttcttgtagc cgagcgatca attacgccga accacgagca accgtcaaaa cagggataaa
     3661 ctgtgacatt gattatgcca aaagcgaaat gaaacaaatt cgcatgctgt atggaaaaga
     3721 cgatcgtgta caagcacact tattgatcca gtcttttcga ccaggagaaa ttaccgctga
     3781 aaaagccaat caactagggg cagagtatgc gaaaaaaata gcccctgacc accaaatcgc
     3841 gatttacaca catacagaca aagaccatat tcataaccac attgtcatta actccgtcaa
     3901 tctggaaact gggaacaaat ttcaagccca tggtcaagca tttttaaaca aatgttatga
     3961 cctaaatgac gagatttgtc ttgaacatga cttaacaatc actgaacgag ggaagaaacc
     4021 cgaaaaacga accatgtctg aaatcaaatt aaaagaaaaa aatgaacctg tttggaaaga
     4081 cgaaattcgg tttgcgattg atcaaacaat gaaaaacaaa aaaactcgaa cgtataacca
     4141 attttgtgat tctcttaaaa cattcggcat tcattgcttg aatcgtggga aaaattttac
     4201 ttacgaattg atccacaaaa agaaaaaagt acgatccaac aaactaggaa aggattacga
     4261 aaaggagacg attttacatg agctggacag acgagaacga gcctacaatc aacaacgaac
     4321 caacgagcta cgaagagctc gagctagcat tcgcgaaact gcaaaagaag tacgaagaga
     4381 acaacgaact cttacgactg aacaaccgga aattagaccg actcgaagaa accatgacca
     4441 acacgttgaa agaggagcag actaccaaca agaattatcg ttctaaaacg ttacaagaca
     4501 tagaaaatga aataaagaaa caacgtgctt ttcttgcacc ttataccaaa gaaagaatac
     4561 aaactacaat tgattcacaa gtcaaaaaat tccaccatgc gctattaaac cagcgaaata
     4621 aagaacagaa aaaagtaatt atgcagcgat caatggatat tcttgccccc ttatgttgct
     4681 taatcatgac actgttagcc ttttggctgg tatggggaga ataaatagaa atggcattct
     4741 atttacccta tctactcatt tttgccagta ttttaggaat tatttggctt agctataagg
     4801 cttatcaaac aagatattca ttaaaaggct ctaaaattcg atttaagagg tttttattgc
     4861 caggggttat atttacatta tcaatcgttt taagtggttt attcggcgtt ttagagggaa
     4921 ataaacgtat ttcaagaagt attttattag gggatatcac tcaaaagtat gaagcagcat
     4981 gtgataaaaa gaaaaaggag caagtgttaa cacaaaaaat ggaagagttt accacttgtt
     5041 atgaggaaat gaacgatatt tttgtgaatc aagaaaaacg tttgacggat aaaaacatgg
     5101 aaaaactcac tcgtctttat caaaacttgc cagaaaaaca gcaaaaagag gttcaagaca
     5161 actatgagcg aaccaaaaaa gacgtgcaat attttaaaga tacgcagaca gaagaagctt
     5221 gttataattt attcagtgat acaatccctt tttcaactag tgaacaggaa cgaaaagaac
     5281 ggcaacaatc agttacctac gaacgttata aagcactgct tcagcaagca acgaacatac
     5341 aaaatccaac gaaaaaagaa acggcattaa attatctaaa aagtgtcaag gaatggttag
     5401 atcagcaaca gcaaaattga atttgatcgg caatcatgtt aaactaaaca tgcaaatgat
     5461 caaacattag atacacgaaa gccccagaga ggtcggattc tctggggctt tttttcaggt
     5521 tgatgtcgcc tttattgatt ttacttcttg tttcggttat tcaaccaata actgaataaa
     5581 gagacacaaa cttctataag aagggggcaa atgaacaatt caaacattag atacacctcc
     5641 ttccagtcgc aagactgtcg gataggcgac aagttattat atcttaaaaa attaaacttg
     5701 tgtggtgttt ttaagtatcg cttattttag ggttgttagg gcttgccctg accgcctgta
     5761 aggcgcttta aagctagata aggattttta tccaagactg tcttaaaacg gcttagataa
     5821 gcattcagaa ccgctcaaag gcctctttac caacatgttt ttagcaaagg agcctttagg
     5881 cgactgcgca gtacaatgtg agagcgtagc gatcacacct ttttggcgac cgtaggaagc
     5941 aaggttttgg attggcagtt ttgaaaaatg cgcgaacctg tttaaagaaa aaagaagtgg
     6001 tttttaggcg ggaaaattag cccccctctt tttatatctc tttttaaacc tctttttaaa
     6061 cctctttacc gtaagctgtg tccttactct accaatggat acagaatgtt atgaaggaca
     6121 ttttgtctgt ttatgaagga cattttgtct gtttatgaag gacattttgt ctgtttatga
     6181 aggacatttt gtctgtttga acgtcaaata tgaatgtctt gacatttaaa aaatgtcatt
     6241 cataattgga ttgaggtgat tat
//
