LOCUS       NZ_CP066471             6267 bp    DNA     circular CON 19-FEB-2024
DEFINITION  Enterococcus faecium strain Dallas 91 plasmid p91_6.2kb, complete
            sequence.
ACCESSION   NZ_CP066471
VERSION     NZ_CP066471.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN17038086
            Assembly: GCF_016406345.1
KEYWORDS    RefSeq.
SOURCE      Enterococcus faecium
  ORGANISM  Enterococcus faecium
            Bacteria; Bacillota; Bacilli; Lactobacillales; Enterococcaceae;
            Enterococcus.
REFERENCE   1  (bases 1 to 6267)
  AUTHORS   Islam,M.J. and Palmer,K.
  TITLE     Molecular characterization of VREfm isolates from Dallas, Texas
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 6267)
  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                   :: 210.0x
            Sequencing Technology :: Illumina NextSeq; Oxford Nanopore MinION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 02/19/2024 04:00:00
            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)                     :: 3,121
            CDSs (total)                      :: 3,030
            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)              :: 112
            CDSs (without protein)            :: 112
            Pseudo Genes (ambiguous residues) :: 0 of 112
            Pseudo Genes (frameshifted)       :: 41 of 112
            Pseudo Genes (incomplete)         :: 65 of 112
            Pseudo Genes (internal stop)      :: 30 of 112
            Pseudo Genes (multiple problems)  :: 20 of 112
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP066471.1.
            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..6267
                     /organism="Enterococcus faecium"
                     /mol_type="genomic DNA"
                     /strain="Dallas 91"
                     /isolation_source="rectal swab"
                     /host="Homo sapiens"
                     /db_xref="taxon:1352"
                     /plasmid="p91_6.2kb"
                     /geo_loc_name="USA: Dallas"
                     /collection_date="2015"
     gene            1..945
                     /locus_tag="JCQ04_RS15445"
                     /old_locus_tag="JCQ04_15445"
     CDS             1..945
                     /locus_tag="JCQ04_RS15445"
                     /old_locus_tag="JCQ04_15445"
                     /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="JCQ04_RS15450"
                     /old_locus_tag="JCQ04_15450"
     CDS             966..1499
                     /locus_tag="JCQ04_RS15450"
                     /old_locus_tag="JCQ04_15450"
                     /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_002321384.1"
                     /translation="MQPQETFTIKELSELFKMSRQAISKHIQKLDSSMIAKNERGYKVV
                     LRSGVLQLARNLGNQMLLDRLHEYEQDNDKNVNIPSKNVVTNKLLDQLREENEFLREQL
                     ALREQNNSHIQKLLDQQQQLTLQANKQIEKLQEKLQLTYTEEAPENDSTTLSEATETID
                     KQIDTEKKWWQLWK"
                     /name="DUF536 domain-containing protein"
     gene            1515..1685
                     /locus_tag="JCQ04_RS15455"
                     /old_locus_tag="JCQ04_15455"
     CDS             1515..1685
                     /locus_tag="JCQ04_RS15455"
                     /old_locus_tag="JCQ04_15455"
                     /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_002292472.1"
                     /translation="MTRKNLLFGSILLGILGFSPMLLSVINKGNKHGELKLNPNYYNSP
                     NEELFVKETDK"
                     /name="hypothetical protein"
     gene            2135..2668
                     /locus_tag="JCQ04_RS15460"
                     /old_locus_tag="JCQ04_15460"
     CDS             2135..2668
                     /locus_tag="JCQ04_RS15460"
                     /old_locus_tag="JCQ04_15460"
                     /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            2680..2883
                     /locus_tag="JCQ04_RS15465"
                     /old_locus_tag="JCQ04_15465"
     CDS             2680..2883
                     /locus_tag="JCQ04_RS15465"
                     /old_locus_tag="JCQ04_15465"
                     /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            3214..3594
                     /locus_tag="JCQ04_RS15470"
                     /old_locus_tag="JCQ04_15470"
     CDS             3214..3594
                     /locus_tag="JCQ04_RS15470"
                     /old_locus_tag="JCQ04_15470"
                     /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            3576..4490
                     /locus_tag="JCQ04_RS15475"
                     /old_locus_tag="JCQ04_15475"
     CDS             3576..4490
                     /locus_tag="JCQ04_RS15475"
                     /old_locus_tag="JCQ04_15475"
                     /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            4735..5424
                     /locus_tag="JCQ04_RS15480"
                     /old_locus_tag="JCQ04_15480"
     CDS             4735..5424
                     /locus_tag="JCQ04_RS15480"
                     /old_locus_tag="JCQ04_15480"
                     /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          3577..4487
                     /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 aacttaggca
     1141 accaaatgtt gctagatagg ttgcacgagt acgaacaaga caacgataaa aatgttaata
     1201 taccaagcaa aaacgtggtt acaaacaagt tgctagatca gttgcgtgaa gaaaatgaat
     1261 ttttacgaga acaacttgcc ctcagagagc aaaataattc tcatatacaa aaactactcg
     1321 accagcaaca acaactcacc ctacaagcca acaaacaaat cgaaaaactg caagaaaaac
     1381 tacagttgac ttatacagaa gaagctccag agaatgactc aacgactctt tctgaagcaa
     1441 cagaaacaat agacaaacaa attgatactg aaaaaaaatg gtggcaactt tggaaataac
     1501 tggagggaac attcatgaca agaaaaaatc ttctattcgg ttctatttta ctaggaattc
     1561 taggattcag tccgatgtta ttgtcagtga tcaataaagg gaataaacat ggtgaattga
     1621 aattgaatcc aaattattac aacagtccta acgaagaatt gtttgtaaaa gaaacagata
     1681 aataataaaa aagactgctc tttcgagcag ccagttaaaa aataatgagt gtttattctt
     1741 gaaaaagcaa cgcgcttatg aagcgctacc aaaaatttat catattttat taaaaataac
     1801 aacccagtaa aaaatgactg gtaaaaattc acaaagaaac ggaaagaagc aaccgcagaa
     1861 aatcaagctt aaaaagagct tttgacctag accaatcgaa aatcacaaag tgagcctctg
     1921 tatcggttga tacaagggct acttggcata gtgtacatta tgtcaacaag aatttaatat
     1981 aacatatttt cctaatgcat tctaactata ccacattatc aaaaatataa attatcttta
     2041 ctaaataaaa tattgacaag cctatacctt ttgttttatg attttcacaa agaaaacgtt
     2101 ttctatatat ttttctgtat caggaggaaa ttctatgaaa aaatttactt taggggtagc
     2161 tttgttaact attggggcag ttgttttacc gtcaactact atagtttatg cttcagaaaa
     2221 ttcccaagtg gtatcattaa acgaaaacaa tgctactgaa aatgtagtta ttgagtacac
     2281 tgaagatggt atggtcgtaa ctaaatatga ggatggttat agtgcggaag attttgcaaa
     2341 ttcttcagat atcatgacaa gagctgcagt tgcaagatgg ggcaaaaagg aatatacaaa
     2401 tattgctgta accactggag tagctgctaa tgctattaat gctgcctttt gggcaggagg
     2461 gaaagctagc acttctatgt ttggtatccc aggttgggca attggtgctt tgttaacagg
     2521 tgcaagttgg actaaaaaag gtgcttctcc agggaatgca gttgcaaaag aatgggacaa
     2581 aaatggtaat ggctggattg gattttatta ccaaagggga tatgatgcag ctggaagagt
     2641 tgtagctact agatattcaa cgttataagt taaggagtga tgtttttgat atctaaatca
     2701 ttaaaatcat taaaaacatt tactaaaaag aatccgcaaa tagctactat tcgtattttt
     2761 atatttgcta tagctgttgc tataattgtt aatatgctaa gcggagggca attatacaaa
     2821 tctggtttat ttttagtgtt aatcttagtt gtcttagaca taataaagtc taaaaaaaaa
     2881 taaatcgata cattttagaa gaatagggtt gtttgaatat tacaaagcaa caatttcacc
     2941 ttcggtgaaa taagcgaaac tttacaaaaa gtggctagca aatgctagcc tttttttgta
     3001 ttgtggagcg tggattttga gggggattca agggggagct tgcgctcctt tgacaagcgg
     3061 ttatttgcac caaatacgga ggtatttggc tagcaaatat agagcttgcc aagcccttta
     3121 gtgagcttta gtgagcttta cttattgtac ctttttaggt acaatggtat tgcgaacgat
     3181 acgtccgtag gacgtactga aagggtggga cttatgagcg aacaaaatca atatttggct
     3241 agcaatcatt ctaaaaaata tacctatcga tccgagccaa aacaaatcag ttttcgagtg
     3301 agcgaatccg aatttgcaaa gctgaagcag tcagctgaag ctttgcaaat gagtgtgccg
     3361 gctttcgtga aagccaaggc acaaaacgcg cgtctggtga caccgaaagt ggcgccagac
     3421 attgctcagg caatcgcgcg cgatttagcc aaagctggcg ggaatatcaa tcaaattgcc
     3481 aagtggtgca acacacacca acacgacgtt gatcctggcg acgcccaacg cttatccgaa
     3541 aacctaaaaa tcatgcaaaa ggagctacaa aagatatggc aacagttaaa gtaagccgaa
     3601 ccacttcttg tagccgagcg atcaattacg ccgaaccacg agcaaccgtc aaaacaggga
     3661 taaactgtga cattgattat gccaaaagcg aaatgaaaca aattcgcatg ctgtatggaa
     3721 aagacgatcg tgtacaagca cacttattga tccagtcttt tcgaccagga gaaattaccg
     3781 ctgaaaaagc caatcaacta ggggcagagt atgcgaaaaa aatagcccct gaccaccaaa
     3841 tcgcgattta cacacataca gacaaagacc atattcataa ccacattgtc attaactccg
     3901 tcaatctgga aactgggaac aaatttcaag cccatggtca agcattttta aacaaatgtt
     3961 atgacctaaa tgacgagatt tgtcttgaac atgacttaac aatcactgaa cgagggaaga
     4021 aacccgaaaa acgaaccatg tctgaaatca aattaaaaga aaaaaatgaa cctgtttgga
     4081 aagacgaaat tcggtttgcg attgatcaaa caatgaaaaa caaaaaaact cgaacgtata
     4141 accaattttg tgattctctt aaaacattcg gcattcattg cttgaatcgt gggaaaaatt
     4201 ttacttacga attgatccac aaaaagaaaa aagtacgatc caacaaacta ggaaaggatt
     4261 acgaaaagga gacgatttta catgagctgg acagacgaga acgagcctac aatcaacaac
     4321 gaaccaacga gctacgaaga gctcgagcta gcattcgcga aactgcaaaa gaagtacgaa
     4381 gagaacaacg aactcttacg actgaacaac cggaaattag accgactcga agaaaccatg
     4441 accaacacgt tgaaagagga gcagactacc aacaagaatt atcgttctaa aacgttacaa
     4501 gacatagaaa atgaaataaa gaaacaacgt gcttttcttg caccttatac caaagaaaga
     4561 atacaaacta caattgattc acaagtcaaa aaattccacc atgcgctatt aaaccagcga
     4621 aataaagaac agaaaaaagt aattatgcag cgatcaatgg atattcttgc ccccttatgt
     4681 tgcttaatca tgacactgtt agccttttgg ctggtatggg gagaataaat agaaatggca
     4741 ttctatttac cctatctact catttttgcc agtattttag gaattatttg gcttagctat
     4801 aaggcttatc aaacaagata ttcattaaaa ggctctaaaa ttcgatttaa gaggttttta
     4861 ttgccagggg ttatatttac attatcaatc gttttaagtg gtttattcgg cgttttagag
     4921 ggaaataaac gtatttcaag aagtatttta ttaggggata tcactcaaaa gtatgaagca
     4981 gcatgtgata aaaagaaaaa ggagcaagtg ttaacacaaa aaatggaaga gtttaccact
     5041 tgttatgagg aaatgaacga tatttttgtg aatcaagaaa aacgtttgac ggataaaaac
     5101 atggaaaaac tcactcgtct ttatcaaaac ttgccagaaa aacagcaaaa agaggttcaa
     5161 gacaactatg agcgaaccaa aaaagacgtg caatatttta aagatacgca gacagaagaa
     5221 gcttgttata atttattcag tgatacaatc cctttttcaa ctagtgaaca ggaacgaaaa
     5281 gaacggcaac aatcagttac ctacgaacgt tataaagcac tgcttcagca agcaacgaac
     5341 atacaaaatc caacgaaaaa agaaacggca ttaaattatc taaaaagtgt caaggaatgg
     5401 ttagatcagc aacagcaaaa ttgaatttga tcggcaatca tgttaaacta aacatgcaaa
     5461 tgatcaaaca ttagatacac gaaagcccca gagaggtcgg attctctggg gctttttttc
     5521 aggttgatgt cgcctttatt gattttactt cttgtttcgg ttattcaacc aataactgaa
     5581 taaagagaca caaacttcta taagaagggg gcaaatgaac aattcaaaca ttagatacac
     5641 ctccttccag tcgcaagact gtcggatagg cgacaagtta ttatatctta aaaaattaaa
     5701 cttgtgtggt gtttttaagt atcgcttatt ttagggttgt tagggcttgc cctgaccgcc
     5761 tgtaaggcgc tttaaagcta gataaggatt tttatccaag actgtcttaa aacggcttag
     5821 ataagcattc agaaccgctc aaaggcctct ttaccaacat gtttttagca aaggagcctt
     5881 taggcgactg cgcagtacaa tgtgagagcg tagcgatcac acctttttgg cgaccgtagg
     5941 aagcaaggtt ttggattggc agttttgaaa aatgcgcgaa cctgtttaaa gaaaaaagaa
     6001 gtggttttta ggcgggaaaa ttagcccccc tctttttata tctcttttta aacctctttt
     6061 taaacctctt taccgtaagc tgtgtcctta ctctaccaat ggatacagaa tgttatgaag
     6121 gacattttgt ctgtttatga aggacatttt gtctgtttat gaaggacatt ttgtctgttt
     6181 atgaaggaca ttttgtctgt ttgaacgtca aatatgaatg tcttgacatt taaaaaatgt
     6241 cattcataat tggattgagg tgattat
//
