LOCUS       NZ_CP066393             6172 bp    DNA     circular CON 20-FEB-2024
DEFINITION  Enterococcus faecium strain Dallas 17_1 plasmid p17_1_6kb, complete
            sequence.
ACCESSION   NZ_CP066393
VERSION     NZ_CP066393.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN17038071
            Assembly: GCF_016406445.1
KEYWORDS    RefSeq.
SOURCE      Enterococcus faecium
  ORGANISM  Enterococcus faecium
            Bacteria; Bacillota; Bacilli; Lactobacillales; Enterococcaceae;
            Enterococcus.
REFERENCE   1  (bases 1 to 6172)
  AUTHORS   Islam,M.J. and Palmer,K.
  TITLE     Molecular characterization of VREfm isolates from Dallas, Texas
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 6172)
  AUTHORS   Islam,M.J. and Palmer,K.
  TITLE     Direct Submission
  JOURNAL   Submitted (20-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                   :: 156.0x
            Sequencing Technology :: Illumina NextSeq; Oxford Nanopore MinION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 02/20/2024 02:48:50
            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)                     :: 3,073
            CDSs (total)                      :: 2,982
            Genes (coding)                    :: 2,859
            CDSs (with protein)               :: 2,859
            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)              :: 123
            CDSs (without protein)            :: 123
            Pseudo Genes (ambiguous residues) :: 0 of 123
            Pseudo Genes (frameshifted)       :: 45 of 123
            Pseudo Genes (incomplete)         :: 78 of 123
            Pseudo Genes (internal stop)      :: 24 of 123
            Pseudo Genes (multiple problems)  :: 20 of 123
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP066393.1.
            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..6172
                     /organism="Enterococcus faecium"
                     /mol_type="genomic DNA"
                     /strain="Dallas 17_1"
                     /isolation_source="rectal swab"
                     /host="Homo sapiens"
                     /db_xref="taxon:1352"
                     /plasmid="p17_1_6kb"
                     /geo_loc_name="USA: Dallas"
                     /collection_date="2015"
     gene            1..945
                     /locus_tag="JCP93_RS15185"
                     /old_locus_tag="JCP93_15185"
     CDS             1..945
                     /locus_tag="JCP93_RS15185"
                     /old_locus_tag="JCP93_15185"
                     /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="JCP93_RS15190"
                     /old_locus_tag="JCP93_15190"
     CDS             966..1499
                     /locus_tag="JCP93_RS15190"
                     /old_locus_tag="JCP93_15190"
                     /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="JCP93_RS15195"
                     /old_locus_tag="JCP93_15195"
     CDS             1514..1684
                     /locus_tag="JCP93_RS15195"
                     /old_locus_tag="JCP93_15195"
                     /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            2138..2362
                     /locus_tag="JCP93_RS15200"
                     /old_locus_tag="JCP93_15200"
     CDS             2138..2362
                     /locus_tag="JCP93_RS15200"
                     /old_locus_tag="JCP93_15200"
                     /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            2382..2669
                     /locus_tag="JCP93_RS15205"
                     /old_locus_tag="JCP93_15205"
     CDS             2382..2669
                     /locus_tag="JCP93_RS15205"
                     /old_locus_tag="JCP93_15205"
                     /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            3119..3499
                     /locus_tag="JCP93_RS15210"
                     /old_locus_tag="JCP93_15210"
     CDS             3119..3499
                     /locus_tag="JCP93_RS15210"
                     /old_locus_tag="JCP93_15210"
                     /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            3481..4395
                     /locus_tag="JCP93_RS15215"
                     /old_locus_tag="JCP93_15215"
     CDS             3481..4395
                     /locus_tag="JCP93_RS15215"
                     /old_locus_tag="JCP93_15215"
                     /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            4640..5329
                     /locus_tag="JCP93_RS15225"
                     /old_locus_tag="JCP93_15225"
     CDS             4640..5329
                     /locus_tag="JCP93_RS15225"
                     /old_locus_tag="JCP93_15225"
                     /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..6172
                     /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          3482..4392
                     /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 gtagtatata cattatgtct actagatctt
     1981 aatataacga ttttataatt taatttaaac gattatgaat tcaaaactac tttttatgac
     2041 gttaatcatt gttatataat aaaatgttat ataataaaat tactaagatt atttaatata
     2101 acaagcaatt ttaaaaaaac gaaaaggaaa aacaatcatg aaaaagaaag tattaaaaca
     2161 ttgtgttatt ctaggaatat taggaacttg tctagctggc atcggtacag gaataaaagt
     2221 tgatgcagct acttactatg gaaatggtct ttattgtaac aaagaaaaat gttgggtaga
     2281 ttggaatcaa gctaaaggag aaattggaaa aattattgtt aatggttggg ttaatcatgg
     2341 tccatgggca cctagaaggt agtggtaggg aggttattat aatggatttt actaaagaag
     2401 aaaaactttt aaatgcaatt agtaaagtat acaatgaagc aactatagat gactatcctg
     2461 acttaaaaga aaagctcttt ctttattcta aagaaatcag tgagggaaaa agtgttggtg
     2521 aagttagtat gaaattaagt agttttcttg gaagatatat tttaaaacat aaatttggat
     2581 tacctaaatc tttaatagaa ttacaagaaa ttgttagtaa ggaatctcaa gtatatagag
     2641 gatgggcttc tattggtatt tggagttaat tctttggaat aaaatgaaaa tgggactgaa
     2701 gaatcaattc tgattcatca gtcccataaa ttatagagcc gaaaaattat catatttata
     2761 gatttattaa tagtaaatgg cataagaatc tttgaacaac gaaaaaaatg tagctctacc
     2821 taattattga tttgcaacaa tttcaccgaa ggtgaaacaa gcgaaacttt acaaaaagtg
     2881 gctagcattt gctagtcttt tttgtattgt ggagagtggg ggggaggggg attcaagggg
     2941 gagcttgcgc ccctttgaca agcggttatt tgcaccaaat acgtaggtat ttggctagca
     3001 aatatagagc ttgccaagcc ctttagtgag ctttagtgag ctttacttat tgtacctttt
     3061 taggtacaat ggtattgcga acgatacgtc cgtaggacgt actgaaaggg tgggacttat
     3121 gagcgaacaa aatcaatatt tggctagcaa tcattctaaa aaatatacct atcgatccga
     3181 gccaaaacaa atcagttttc gagtgagcga atccgaattt gcaaagctga agcagtcagc
     3241 tgaagctttg caaatgagtg tgccggcttt cgtgaaagcc aaggcacaaa acgcgcgtct
     3301 ggtgacaccg aaagtggcgc cagacattgc tcaggcaatc gcgcgcgatt tagccaaagc
     3361 tggcgggaat atcaatcaaa ttgccaagtg gtgcaacaca caccaacacg acgttgatcc
     3421 tggcgacgcc caacgcttat ccgaaaacct aaaaatcatg caaaaggagc tacaaaagat
     3481 atggcaacag ttaaagtaag ccgaaccact tcttgtagcc gagcgatcaa ttacgccgaa
     3541 ccacgagcaa ccgtcaaaac agggataaac tgtgacattg attatgccaa aagcgaaatg
     3601 aaacaaattc gcatgctgta tggaaaagac gatcgtgtac aagcacactt attgatccag
     3661 tcttttcgac caggagaaat taccgctgaa aaagccaatc aactaggggc agagtatgcg
     3721 aaaaaaatag cccctgacca ccaaatcgcg atttacacac atacagacaa agaccatatt
     3781 cataaccaca ttgtcattaa ctccgtcaat ctggaaactg ggaacaaatt tcaagcccat
     3841 ggtcaagcat ttttaaacaa atgttatgac ctaaatgacg agatttgtct tgaacatgac
     3901 ttaacaatca ctgaacgagg gaagaaaccc gaaaaacgaa ccatgtctga aatcaaatta
     3961 aaagaaaaaa atgaacctgt ttggaaagac gaaattcggt ttgcgattga tcaaacaatg
     4021 aaaaacaaaa aaactcgaac gtataaccaa ttttgtgatt ctcttaaaac attcggcatt
     4081 cattgcttga atcgtgggaa aaattttact tacgaattga tccacaaaaa gaaaaaagta
     4141 cgatccaaca aactaggaaa ggattacgaa aaggagacga ttttacatga gctggacaga
     4201 cgagaacgag cctacaatca acaacgaacc aacgagctac gaagagctcg agctagcatt
     4261 cgcgaaactg caaaagaagt acgaagagaa caacgaactc ttacgactga acaaccggaa
     4321 attagaccga ctcgaagaaa ccatgaccaa cacgttgaaa gaggagcaga ctaccaacaa
     4381 gaattatcgt tctaaaacgt tacaagacat agaaaatgaa ataaagaaac aacgtgcttt
     4441 tcttgcacct tataccaaag aaagaataca aactacaatt gattcacaag tcaaaaaatt
     4501 ccaccatgcg ctattaaacc agcgaaataa agaacagaaa aaagtaatta tgcagcgatc
     4561 aatggatatt cttgccccct tatgttgctt aatcatgaca ctgttagcct tttggctggt
     4621 atggggagaa taaatagaaa tggcattcta tttaccctat ctactcattt ttgccagtat
     4681 tttaggaatt atttggctta gctataaggc ttatcaaaca agatattcat taaaaggctc
     4741 taaaattcga tttaagaggt ttttattgcc aggggttata tttacattat caatcgtttt
     4801 aagtggttta ttcggcgttt tagagggaaa taaacgtatt tcaagaagta ttttattagg
     4861 ggatatcact caaaagtatg aagcagcatg tgataaaaag aaaaaggagc aagtgttaac
     4921 acaaaaaatg gaagagttta ccacttgtta tgaggaaatg aacgatattt ttgtgaatca
     4981 agaaaaacgt ttgacggata aaaacatgga aaaactcact cgtctttatc aaaacttgcc
     5041 agaaaaacag caaaaagagg ttcaagacaa ctatgagcga accaaaaaag acgtgcaata
     5101 ttttaaagat acgcagacag aagaagcttg ttataattta ttcagtgata caatcccttt
     5161 ttcaactagt gaacaggaac gaaaagaacg gcaacaatca gttacctacg aacgttataa
     5221 agcactgctt cagcaagcaa cgaacataca aaatccaacg aaaaaagaaa cggcattaaa
     5281 ttatctaaaa agtgtcaagg aatggttaga tcagcaacag caaaattgaa tttgatcggc
     5341 aatcatgtta aactaaacat gcaaatgatc aaacattaga tacacgaaag ccccagagag
     5401 gtcggattct ctggggcttt ttttcaggtt gatgtcgcct ttattgattt tacttcttgt
     5461 ttcggttatt caaccaataa ctgaataaag agacacaaac ttctataaga agggggcaaa
     5521 tgaacaattc aaacattaga tacacctcct tccagtcgca agactgtcgg ataggcgaca
     5581 agttattata tcttaaaaaa ttaaacttgt gtggtgtttt taagtatcgc ttattttagg
     5641 gttgttaggg cttgccctga ccgcctgtaa ggcgctttaa agctagataa ggatttttat
     5701 ccaagactgt cttaaaacgg cttagataag cattcagaac cgctcaaagg cctctttacc
     5761 aacatgtttt tagcaaagga gcctttaggc gactgcgcag tacaatgtga gagcgtagcg
     5821 atcacacctt tttggcgacc gtaggaagca aggttttgga ttggcagttt tgaaaaatgc
     5881 gcgaacctgt ttaaagaaaa aagaagtggt ttttaggcgg gaaaattagc ccccctcttt
     5941 ttatatctct ttttaaacct ctttttaaac ctctttaccg taagctgtgt ccttactcta
     6001 ccaatggata cagaatgtta tgaaggacat tttgtctgtt tatgaaggac attttgtctg
     6061 tttatgaagg acattttgtc tgtttatgaa ggacattttg tctgtttgaa cgtcaaatat
     6121 gaatgtcttg acatttaaaa aatgtcattc ataattggat tgaggtgatt at
//
