LOCUS       NZ_CP066572             6168 bp    DNA     circular CON 20-FEB-2024
DEFINITION  Enterococcus faecium strain Dallas 97_1 plasmid p97_1_6kb, complete
            sequence.
ACCESSION   NZ_CP066572
VERSION     NZ_CP066572.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN17038090
            Assembly: GCF_016415025.1
KEYWORDS    RefSeq.
SOURCE      Enterococcus faecium
  ORGANISM  Enterococcus faecium
            Bacteria; Bacillota; Bacilli; Lactobacillales; Enterococcaceae;
            Enterococcus.
REFERENCE   1  (bases 1 to 6168)
  AUTHORS   Islam,M.J. and Palmer,K.
  TITLE     Molecular characterization of VREfm isolates from Dallas, Texas
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 6168)
  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                   :: 66.0x
            Sequencing Technology :: Illumina NextSeq; Oxford Nanopore MinION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 02/20/2024 02:46:30
            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)                     :: 3,203
            CDSs (total)                      :: 3,112
            Genes (coding)                    :: 2,949
            CDSs (with protein)               :: 2,949
            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)              :: 163
            CDSs (without protein)            :: 163
            Pseudo Genes (ambiguous residues) :: 0 of 163
            Pseudo Genes (frameshifted)       :: 73 of 163
            Pseudo Genes (incomplete)         :: 87 of 163
            Pseudo Genes (internal stop)      :: 37 of 163
            Pseudo Genes (multiple problems)  :: 30 of 163
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP066572.1.
            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..6168
                     /organism="Enterococcus faecium"
                     /mol_type="genomic DNA"
                     /strain="Dallas 97_1"
                     /isolation_source="rectal swab"
                     /host="Homo sapiens"
                     /db_xref="taxon:1352"
                     /plasmid="p97_1_6kb"
                     /geo_loc_name="USA: Dallas"
                     /collection_date="2015"
     gene            1..945
                     /locus_tag="JCP88_RS15765"
                     /old_locus_tag="JCP88_15765"
     CDS             1..945
                     /locus_tag="JCP88_RS15765"
                     /old_locus_tag="JCP88_15765"
                     /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="JCP88_RS15770"
                     /old_locus_tag="JCP88_15770"
     CDS             966..1499
                     /locus_tag="JCP88_RS15770"
                     /old_locus_tag="JCP88_15770"
                     /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="JCP88_RS15775"
                     /old_locus_tag="JCP88_15775"
     CDS             1514..1684
                     /locus_tag="JCP88_RS15775"
                     /old_locus_tag="JCP88_15775"
                     /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_165353901.1"
                     /translation="MTKKHLLFGSILLGILSFSPMLLSVANKGNKKGELKLNPNYYNSP
                     NEELFVKETDK"
                     /name="hypothetical protein"
     gene            2134..2358
                     /locus_tag="JCP88_RS15780"
                     /old_locus_tag="JCP88_15780"
     CDS             2134..2358
                     /locus_tag="JCP88_RS15780"
                     /old_locus_tag="JCP88_15780"
                     /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            2378..2665
                     /locus_tag="JCP88_RS15785"
                     /old_locus_tag="JCP88_15785"
     CDS             2378..2665
                     /locus_tag="JCP88_RS15785"
                     /old_locus_tag="JCP88_15785"
                     /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            3115..3495
                     /locus_tag="JCP88_RS15790"
                     /old_locus_tag="JCP88_15790"
     CDS             3115..3495
                     /locus_tag="JCP88_RS15790"
                     /old_locus_tag="JCP88_15790"
                     /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            3477..4391
                     /locus_tag="JCP88_RS15795"
                     /old_locus_tag="JCP88_15795"
     CDS             3477..4391
                     /locus_tag="JCP88_RS15795"
                     /old_locus_tag="JCP88_15795"
                     /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            4636..5325
                     /locus_tag="JCP88_RS15800"
                     /old_locus_tag="JCP88_15800"
     CDS             4636..5325
                     /locus_tag="JCP88_RS15800"
                     /old_locus_tag="JCP88_15800"
                     /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..6168
                     /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          3478..4388
                     /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 acagtcctaa cgaagaattg tttgtaaaag aaacggataa
     1681 ataataaaaa agactgctct tccgagcagc cagttaaaaa ataatgagtg tttattcttg
     1741 aaaaagcaac gcgcttatga agcgctacca aaaatttatc atattttatg aaaaataaca
     1801 ccccagtaaa aaatgactgg taaaaattca caaagaaacg gaaagaagca actgcagaaa
     1861 atcaagcctt aaaaagagct tttgacctag accaattaaa aatcacaaag tgagcgtctc
     1921 tatccattgg tagaggggct acttggcata gtatacatta tgtctactag ctgtttaaat
     1981 aactgatctt ataattttat ttaaacgatt atgaattcaa aactactttt tatgacgtta
     2041 atcattgtta tataataaaa tgttatataa taaaattact aagattattt aatataacaa
     2101 gcaattttaa aaaaacgaaa aggaaaaaca atcatgaaaa agaaagtatt aaaacattgt
     2161 gttattctag gaatattagg aacttgtcta gctggcatcg gtacaggaat aaaagttgat
     2221 gcagctactt actatggaaa tggtctttat tgtaacaaag aaaaatgttg ggtagattgg
     2281 aatcaagcta aaggagaaat tggaaaaatt attgttaatg gttgggttaa tcatggtcca
     2341 tgggcaccta gaaggtagtg gtagggaggt tattataatg gattttacta aagaagaaaa
     2401 acttttaaat gcaattagta aagtatacaa tgaagcaact atagatgact atcctgactt
     2461 aaaagaaaag ctctttcttt attctaaaga aatcagtgag ggaaaaagtg ttggtgaagt
     2521 tagtatgaaa ttaagtagtt ttcttggaag atatatttta aaacataaat ttggattacc
     2581 taaatcttta atagaattac aagaaattgt tagtaaggaa tctcaagtat atagaggatg
     2641 ggcttctatt ggtatttgga gttaattctt tggaataaaa tgaaaatggg actgaagaat
     2701 caattctgat tcatcagtcc cataaattat agagccgaaa aattatcata tttatagatt
     2761 tattaatagt aaatggcata agaatctttg aacaacgaaa aaaatgtagc tctacctaat
     2821 tattgatttg caacaatttc accgaaggtg aaacaagcga aactttacaa aaagtggcta
     2881 gcatttgcta gtcttttttg tattgtggag agtggggggg agggggattc aagggggagc
     2941 ttgcgcccct ttgacaagcg gttatttgca ccaaatacgt aggtatttgg ctagcaaata
     3001 tagagcttgc caagcccttt agtgagcttt agtgagcttt acttattgta cctttttagg
     3061 tacaatggta ttgcgaacga tacgtccgta ggacgtactg aaagggtggg acttatgagc
     3121 gaacaaaatc aatatttggc tagcaatcat tctaaaaaat atacctatcg atccgagcca
     3181 aaacaaatca gttttcgagt gagcgaatcc gaatttgcaa agctgaagca gtcagctgaa
     3241 gctttgcaaa tgagtgtgcc ggctttcgtg aaagccaagg cacaaaacgc gcgtctggtg
     3301 acaccgaaag tggcgccaga cattgctcag gcaatcgcgc gcgatttagc caaagctggc
     3361 gggaatatca atcaaattgc caagtggtgc aacacacacc aacacgacgt tgatcctggc
     3421 gacgcccaac gcttatccga aaacctaaaa atcatgcaaa aggagctaca aaagatatgg
     3481 caacagttaa agtaagccga accacttctt gtagccgagc gatcaattac gccgaaccac
     3541 gagcaaccgt caaaacaggg ataaactgtg acattgatta tgccaaaagc gaaatgaaac
     3601 aaattcgcat gctgtatgga aaagacgatc gtgtacaagc acacttattg atccagtctt
     3661 ttcgaccagg agaaattacc gctgaaaaag ccaatcaact aggggcagag tatgcgaaaa
     3721 aaatagcccc tgaccaccaa atcgcgattt acacacatac agacaaagac catattcata
     3781 accacattgt cattaactcc gtcaatctgg aaactgggaa caaatttcaa gcccatggtc
     3841 aagcattttt aaacaaatgt tatgacctaa atgacgagat ttgtcttgaa catgacttaa
     3901 caatcactga acgagggaag aaacccgaaa aacgaaccat gtctgaaatc aaattaaaag
     3961 aaaaaaatga acctgtttgg aaagacgaaa ttcggtttgc gattgatcaa acaatgaaaa
     4021 acaaaaaaac tcgaacgtat aaccaatttt gtgattctct taaaacattc ggcattcatt
     4081 gcttgaatcg tgggaaaaat tttacttacg aattgatcca caaaaagaaa aaagtacgat
     4141 ccaacaaact aggaaaggat tacgaaaagg agacgatttt acatgagctg gacagacgag
     4201 aacgagccta caatcaacaa cgaaccaacg agctacgaag agctcgagct agcattcgcg
     4261 aaactgcaaa agaagtacga agagaacaac gaactcttac gactgaacaa ccggaaatta
     4321 gaccgactcg aagaaaccat gaccaacacg ttgaaagagg agcagactac caacaagaat
     4381 tatcgttcta aaacgttaca agacatagaa aatgaaataa agaaacaacg tgcttttctt
     4441 gcaccttata ccaaagaaag aatacaaact acaattgatt cacaagtcaa aaaattccac
     4501 catgcgctat taaaccagcg aaataaagaa cagaaaaaag taattatgca gcgatcaatg
     4561 gatattcttg cccccttatg ttgcttaatc atgacactgt tagccttttg gctggtatgg
     4621 ggagaataaa tagaaatggc attctattta ccctatctac tcatttttgc cagtatttta
     4681 ggaattattt ggcttagcta taaggcttat caaacaagat attcattaaa aggctctaaa
     4741 attcgattta agaggttttt attgccaggg gttatattta cattatcaat cgttttaagt
     4801 ggtttattcg gcgttttaga gggaaataaa cgtatttcaa gaagtatttt attaggggat
     4861 atcactcaaa agtatgaagc agcatgtgat aaaaagaaaa aggagcaagt gttaacacaa
     4921 aaaatggaag agtttaccac ttgttatgag gaaatgaacg atatttttgt gaatcaagaa
     4981 aaacgtttga cggataaaaa catggaaaaa ctcactcgtc tttatcaaaa cttgccagaa
     5041 aaacagcaaa aagaggttca agacaactat gagcgaacca aaaaagacgt gcaatatttt
     5101 aaagatacgc agacagaaga agcttgttat aatttattca gtgatacaat ccctttttca
     5161 actagtgaac aggaacgaaa agaacggcaa caatcagtta cctacgaacg ttataaagca
     5221 ctgcttcagc aagcaacgaa catacaaaat ccaacgaaaa aagaaacggc attaaattat
     5281 ctaaaaagtg tcaaggaatg gttagatcag caacagcaaa attgaatttg atcggcaatc
     5341 atgttaaact aaacatgcaa atgatcaaac attagataca cgaaagcccc agagaggtcg
     5401 gattctctgg ggcttttttt caggttgatg tcgcctttat tgattttact tcttgtttcg
     5461 gttattcaac caataactga ataaagagac acaaacttct ataagaaggg ggcaaatgaa
     5521 caattcaaac attagataca cctccttcca gtcgcaagac tgtcggatag gcgacaagtt
     5581 attatatctt aaaaaattaa acttgtgtgg tgtttttaag tatcgcttat tttagggttg
     5641 ttagggcttg ccctgaccgc ctgtaaggcg ctttaaagct agataaggat ttttatccaa
     5701 gactgtctta aaacggctta gataagcatt cagaaccgct caaaggcctc tttaccaaca
     5761 tgtttttagc aaaggagcct ttaggcgact gcgcagtaca atgtgagagc gtagcgatca
     5821 cacctttttg gcgaccgtag gaagcaaggt tttggattgg cagttttgaa aaatgcgcga
     5881 acctgtttaa agaaaaaaga agtggttttt aggcgggaaa attagccccc ctctttttat
     5941 atctcttttt aaacctcttt ttaaacctct ttaccgtaag ctgtgtcctt actctaccaa
     6001 tggatacaga atgttatgaa ggacattttg tctgtttatg aaggacattt tgtctgttta
     6061 tgaaggacat tttgtctgtt tatgaaggac attttgtctg tttgaacgtc aaatatgaat
     6121 gtcttgacat ttaaaaaatg tcattcataa ttggattgag gtgattat
//
