LOCUS       NZ_CP065552             6258 bp    DNA     circular CON 14-FEB-2024
DEFINITION  Enterococcus faecium strain Dallas 1 plasmid p1_6.2kb, complete
            sequence.
ACCESSION   NZ_CP065552
VERSION     NZ_CP065552.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN17012772
            Assembly: GCF_015999605.1
KEYWORDS    RefSeq.
SOURCE      Enterococcus faecium
  ORGANISM  Enterococcus faecium
            Bacteria; Bacillota; Bacilli; Lactobacillales; Enterococcaceae;
            Enterococcus.
REFERENCE   1  (bases 1 to 6258)
  AUTHORS   Islam,M.J.
  TITLE     Molecular characterization of VREfm isolates from Dallas, Texas
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 6258)
  AUTHORS   Islam,M.J.
  TITLE     Direct Submission
  JOURNAL   Submitted (06-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                   :: 30.0x
            Sequencing Technology :: Oxford Nanopore MinION; Illumina NextSeq
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 02/14/2024 02:49:01
            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)                     :: 3,130
            CDSs (total)                      :: 3,039
            Genes (coding)                    :: 2,927
            CDSs (with protein)               :: 2,927
            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)       :: 40 of 112
            Pseudo Genes (incomplete)         :: 66 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
            CP065552.1.
            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..6258
                     /organism="Enterococcus faecium"
                     /mol_type="genomic DNA"
                     /strain="Dallas 1"
                     /isolation_source="Rectal swab"
                     /host="Homo sapiens"
                     /db_xref="taxon:1352"
                     /plasmid="p1_6.2kb"
                     /geo_loc_name="USA: Dallas"
                     /collection_date="2015"
     gene            1..945
                     /locus_tag="I7089_RS15500"
                     /old_locus_tag="I7089_15505"
     CDS             1..945
                     /locus_tag="I7089_RS15500"
                     /old_locus_tag="I7089_15505"
                     /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="I7089_RS15505"
                     /old_locus_tag="I7089_15510"
     CDS             966..1499
                     /locus_tag="I7089_RS15505"
                     /old_locus_tag="I7089_15510"
                     /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="I7089_RS15510"
                     /old_locus_tag="I7089_15515"
     CDS             1515..1685
                     /locus_tag="I7089_RS15510"
                     /old_locus_tag="I7089_15515"
                     /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="I7089_RS15515"
                     /old_locus_tag="I7089_15520"
     CDS             2135..2668
                     /locus_tag="I7089_RS15515"
                     /old_locus_tag="I7089_15520"
                     /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="I7089_RS15520"
                     /old_locus_tag="I7089_15525"
     CDS             2680..2883
                     /locus_tag="I7089_RS15520"
                     /old_locus_tag="I7089_15525"
                     /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            3205..3585
                     /locus_tag="I7089_RS15525"
                     /old_locus_tag="I7089_15530"
     CDS             3205..3585
                     /locus_tag="I7089_RS15525"
                     /old_locus_tag="I7089_15530"
                     /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            3567..4481
                     /locus_tag="I7089_RS15530"
                     /old_locus_tag="I7089_15535"
     CDS             3567..4481
                     /locus_tag="I7089_RS15530"
                     /old_locus_tag="I7089_15535"
                     /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            4726..5415
                     /locus_tag="I7089_RS15540"
                     /old_locus_tag="I7089_15545"
     CDS             4726..5415
                     /locus_tag="I7089_RS15540"
                     /old_locus_tag="I7089_15545"
                     /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          3568..4478
                     /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 aaaccctttt
     3121 agtgagcttt actcattgta cctttttagg tacaatggta ttgcgaacga tacgtccgta
     3181 ggacgtactg aaagggtggg acttatgagc gaacaacatc aaaatttggc tagcgatcat
     3241 tctaaaaaat atacctatcg atccgagcca aaacaaatca gttttcgagt gagcgaatcc
     3301 gaatttgcaa agctgaagca gtcagctgaa gctttgcaaa tgagtgtgcc ggctttcgtg
     3361 aaagccaagg cacaaaacgc gcgtctggtg acaccgaaag tggcgccaga cattgctcag
     3421 gcaatcgcgc gcgatttagc caaagctggc gggaatatca atcaaattgc caagtggtgc
     3481 aacacacacc aacacgacgt tgatcctggc gacgcccaac gcttatccga aaacctaaaa
     3541 atcatgcaaa aggagctaca aaagatatgg caacagttaa agtaagccga accacttctt
     3601 gtagccgagc gatcaattac gccgaaccac gagcaaccgt caaaacaggg ataaactgtg
     3661 acattgatta tgccaaaagc gaaatgaaac aaattcgcat gctgtatgga aaagacgatc
     3721 gtgtacaagc acacttattg atccagtctt ttcgaccagg agaaattacc gctgaaaaag
     3781 ccaatcaact aggggcagag tatgcgaaaa aaatagcccc tgaccaccaa atcgcgattt
     3841 acacacatac agacaaagac catattcata accacattgt cattaactcc gtcaatctgg
     3901 aaactgggaa caaatttcaa gcccatggtc aagcattttt aaacaaatgt tatgacctaa
     3961 atgacgagat ttgtcttgaa catgacttaa caatcactga acgagggaag aaacccgaaa
     4021 aacgaaccat gtctgaaatc aaattaaaag aaaaaaatga acctgtttgg aaagacgaaa
     4081 ttcggtttgc gattgatcaa acaatgaaaa acaaaaaaac tcgaacgtat aaccaatttt
     4141 gtgattctct taaaacattc ggcattcatt gcttgaatcg tgggaaaaat tttacttacg
     4201 aattgatcca caaaaagaaa aaagtacgat ccaacaaact aggaaaggat tacgaaaagg
     4261 agacgatttt acatgagctg gacagacgag aacgagccta caatcaacaa cgaaccaacg
     4321 agctacgaag agctcgagct agcattcgcg aaactgcaaa agaagtacga agagaacaac
     4381 gaactcttac gactgaacaa ccggaaatta gaccgactcg aagaaaccat gaccaacacg
     4441 ttgaaagagg agcagactac caacaagaat tatcgttcta aaacgttaca agacatagaa
     4501 aatgaaataa agaaacaacg tgcttttctt gcaccttata ccaaagaaag aatacaaact
     4561 acaattgatt cacaagtcaa aaaattccac catgcgctat taaaccagcg aaataaagaa
     4621 cagaaaaaag taattatgca gcgatcaatg gatattcttg cccccttatg ttgcttaatc
     4681 atgacactgt tagccttttg gctggtatgg ggagaataaa tagaaatggc attctattta
     4741 ccctatctac tcatttttgc cagtatttta ggaattattt ggcttagcta taaggcttat
     4801 caaacaagat attcattaaa aggctctaaa attcgattta agaggttttt attgccaggg
     4861 gttatattta cattatcaat cgttttaagt ggtttattcg gcgttttaga gggaaataaa
     4921 cgtatttcaa gaagtatttt attaggggat atcactcaaa agtatgaagc agcatgtgat
     4981 aaaaagaaaa aggagcaagt gttaacacaa aaaatggaag agtttaccac ttgttatgag
     5041 gaaatgaacg atatttttgt gaatcaagaa aaacgtttga cggataaaaa catggaaaaa
     5101 ctcactcgtc tttatcaaaa cttgccagaa aaacagcaaa aagaggttca agacaactat
     5161 gagcgaacca aaaaagacgt gcaatatttt aaagatacgc agacagaaga agcttgttat
     5221 aatttattca gtgatacaat ccctttttca actagtgaac aggaacgaaa agaacggcaa
     5281 caatcagtta cctacgaacg ttataaagca ctgcttcagc aagcaacgaa catacaaaat
     5341 ccaacgaaaa aagaaacggc attaaattat ctaaaaagtg tcaaggaatg gttagatcag
     5401 caacagcaaa attgaatttg atcggcaatc atgttaaact aaacatgcaa atgatcaaac
     5461 attagataca cgaaagcccc agagaggtcg gattctctgg ggcttttttt caggttgatg
     5521 tcgcctttat tgattttact tcttgtttcg gttattcaac caataactga ataaagagac
     5581 acaaacttct ataagaaggg ggcaaatgaa caattcaaac attagataca cctccttcca
     5641 gtcgcaagac tgtcggatag gcgacaagtt attatatctt aaaaaattaa acttgtgtgg
     5701 tgtttttaag tatcgcttat tttagggttg ttagggcttg ccctgaccgc ctgtaaggcg
     5761 ctttaaagct agataaggat ttttatccaa gactgtctta aaacggctta gataagcatt
     5821 cagaaccgct caaaggcctc tttaccaaca tgtttttagc aaaggagcct ttaggcgact
     5881 gcgcagtaca atgtgagagc gtagcgatca cacctttttg gcgaccgtag gaagcaaggt
     5941 tttggattgg cagttttgaa aaatgcgcga acctgtttaa agaaaaaaga agtggttttt
     6001 aggcgggaaa attagccccc ctctttttat atctcttttt aaacctcttt ttaaacctct
     6061 ttaccgtaag ctgtgtcctt actctaccaa tggatacaga atgttatgaa ggacattttg
     6121 tctgtttatg aaggacattt tgtctgttta tgaaggacat tttgtctgtt tatgaaggac
     6181 attttgtctg tttgaacgtc aaatatgaat gtcttgacat ttaaaaaatg tcattcataa
     6241 ttggattgag gtgattat
//
