LOCUS       NZ_CP066484             6303 bp    DNA     circular CON 20-FEB-2024
DEFINITION  Enterococcus faecium strain Dallas 93_3 plasmid p93_3_6.3kb,
            complete sequence.
ACCESSION   NZ_CP066484
VERSION     NZ_CP066484.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN17038089
            Assembly: GCF_016406585.1
KEYWORDS    RefSeq.
SOURCE      Enterococcus faecium
  ORGANISM  Enterococcus faecium
            Bacteria; Bacillota; Bacilli; Lactobacillales; Enterococcaceae;
            Enterococcus.
REFERENCE   1  (bases 1 to 6303)
  AUTHORS   Islam,M.J. and Palmer,K.
  TITLE     Molecular characterization of VREfm isolates from Dallas, Texas
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 6303)
  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                   :: 302.0x
            Sequencing Technology :: Illumina NextSeq; Oxford Nanopore MinION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 02/20/2024 02:52:36
            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)                     :: 3,103
            CDSs (total)                      :: 3,012
            Genes (coding)                    :: 2,902
            CDSs (with protein)               :: 2,902
            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)              :: 110
            CDSs (without protein)            :: 110
            Pseudo Genes (ambiguous residues) :: 0 of 110
            Pseudo Genes (frameshifted)       :: 41 of 110
            Pseudo Genes (incomplete)         :: 65 of 110
            Pseudo Genes (internal stop)      :: 27 of 110
            Pseudo Genes (multiple problems)  :: 19 of 110
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP066484.1.
            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..6303
                     /organism="Enterococcus faecium"
                     /mol_type="genomic DNA"
                     /strain="Dallas 93_3"
                     /isolation_source="rectal swab"
                     /host="Homo sapiens"
                     /db_xref="taxon:1352"
                     /plasmid="p93_3_6.3kb"
                     /geo_loc_name="USA: Dallas"
                     /collection_date="2015"
     gene            join(5414..6303,1..61)
                     /locus_tag="JCP71_RS15360"
                     /old_locus_tag="JCP71_15360"
     CDS             join(5414..6303,1..61)
                     /locus_tag="JCP71_RS15360"
                     /old_locus_tag="JCP71_15360"
                     /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_033642128.1"
                     /translation="MANEIVKYHHELNTIPLRKFTPVEMNLFFSIVSRMREKGDKTVRL
                     TFDQLKDLSNYKATANNRFINDLEMTYDKLMDLRFGKRSANGLDIDRFVMFSEFKIRGT
                     AKDPYVDIQVYEKALPLLNNLDEWVRYSLQQFNELQSSYAKTMFRLLKQYRTKGFAYFS
                     KEDFHELLDIPKSYWNNQANVDNRVIKPIRQELTAIFKGLSIKKKYGKGRGKPVVGYQF
                     TFKPEIKKADDFNKHAPTKEEQNKALALADKQKEYEEPATTINEKIKQKKRELELLQQI
                     KQLEKEKEALEKQTESALSKKEKKSLLSDLDNLFQ"
                     /name="replication initiation protein"
     gene            82..615
                     /locus_tag="JCP71_RS15365"
                     /old_locus_tag="JCP71_15365"
     CDS             82..615
                     /locus_tag="JCP71_RS15365"
                     /old_locus_tag="JCP71_15365"
                     /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            631..801
                     /locus_tag="JCP71_RS15370"
                     /old_locus_tag="JCP71_15370"
     CDS             631..801
                     /locus_tag="JCP71_RS15370"
                     /old_locus_tag="JCP71_15370"
                     /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            1251..1784
                     /locus_tag="JCP71_RS15375"
                     /old_locus_tag="JCP71_15375"
     CDS             1251..1784
                     /locus_tag="JCP71_RS15375"
                     /old_locus_tag="JCP71_15375"
                     /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            1796..1999
                     /locus_tag="JCP71_RS15380"
                     /old_locus_tag="JCP71_15380"
     CDS             1796..1999
                     /locus_tag="JCP71_RS15380"
                     /old_locus_tag="JCP71_15380"
                     /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            2321..2701
                     /locus_tag="JCP71_RS15385"
                     /old_locus_tag="JCP71_15385"
     CDS             2321..2701
                     /locus_tag="JCP71_RS15385"
                     /old_locus_tag="JCP71_15385"
                     /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_002321381.1"
                     /translation="MSEQHQNLASDHSKKYTYRSEPKQISFRVSESEFAKLKQSAEALQ
                     MSVPAFVKAKAQNARLVTPKVAPDIAQAIARDLAKAGGNINQIAKWCNTHQHDVAPDDA
                     QRLSENLKIMQKELQKIWQQLK"
                     /name="MobC family plasmid mobilization relaxosome protein"
     gene            2683..3597
                     /locus_tag="JCP71_RS15390"
                     /old_locus_tag="JCP71_15390"
     CDS             2683..3597
                     /locus_tag="JCP71_RS15390"
                     /old_locus_tag="JCP71_15390"
                     /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_002321380.1"
                     /translation="MATVKVSRTTSCSRAINYAEPRATVKTGINCDIDYAKSEMKQIRT
                     LYGKDDRVQAHLLIQSFRPGEITAEKANQLGAEYAKKIAPNHQIAIYTHTDKDHIHNHI
                     VINSVNLETGKKFQAHGQAFLNKCYDLNDEICLEHDLTITERGKKTEKRTMSEIKLKEK
                     NEPVWKDEIRFAIDQTMKNKKTRTYTQFCDSLKTFGIHCLNRGKNFTYELVHKKKKVRS
                     NKLGKDYEKETILHELDRRERTYNQQRTNELRRARASIRETAEEVRREQRTFTPEQSEI
                     RPTRRNHEQHVERGTDHQQELSL"
                     /name="relaxase/mobilization nuclease domain-containing
                     protein"
     gene            3842..4531
                     /locus_tag="JCP71_RS15395"
                     /old_locus_tag="JCP71_15395"
     CDS             3842..4531
                     /locus_tag="JCP71_RS15395"
                     /old_locus_tag="JCP71_15395"
                     /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_002321377.1"
                     /translation="MAFYLPYLLISASILGIIWLSYKAYQTRYSLKGSKIRFKRFLLVG
                     VIFALSIVLSGLFGVLEGNKRVSRSILLGDITQKYEAACDKKKKEQALAQKMEEFTACY
                     EDMNNIFVDQEKRLTDKNMKKLTRFYQNLPEKQQKEVQEKYEQVKKDVQYFKDTQTEEA
                     CCNLFSDTIPFSTSEQERKERQQSVTYERYETLLQQATNIQNPTKKETALNYLESVKEW
                     LDQQQQN"
                     /name="hypothetical protein"
     Typing          5416..6303
                     /name="rep_cluster_1197"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="84.04"
                     /coverage="99.0"
                     /evalue="0.0"
     Typing          2684..3594
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="94.079"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 cgcactttcg aaaaaagaga aaaaaagttt attatctgat ttagataatt tattccagta
       61 gcaacctagg aggcaaccag tatgcaacca caagaaacct ttacaataaa ggaattgtca
      121 gaacttttta agatgagtag gcaagcaata tcgaaacata tccaaaaatt agattcttcc
      181 atgatagcta aaaatgagcg tggttataag gttgtattgc gttctggagt attgcaactt
      241 gctcgcaact taggcaacca aatgttgcta gataggttgc acgagtacga acaagacaac
      301 gataaaaatg ttaatatacc aagcaaaaac gtggttacaa acaagttgct agatcagttg
      361 cgtgaagaaa atgaattttt acgagaacaa cttgccctca gagagcaaaa taattctcat
      421 atacaaaaac tactcgacca gcaacaacaa ctcaccctac aagccaacaa acaaatcgaa
      481 aaactgcaag aaaaactaca gttgacttat acagaagaag ctccagagaa tgactcaacg
      541 actctttctg aagcaacaga aacaatagac aaacaaattg atactgaaaa aaaatggtgg
      601 caactttgga aataactgga gggaacattc atgacaagaa aaaatcttct attcggttct
      661 attttactag gaattctagg attcagtccg atgttattgt cagtgatcaa taaagggaat
      721 aaacatggtg aattgaaatt gaatccaaat tattacaaca gtcctaacga agaattgttt
      781 gtaaaagaaa cagataaata ataaaaaaga ctgctctttc gagcagccag ttaaaaaata
      841 atgagtgttt attcttgaaa aagcaacgcg cttatgaagc gctaccaaaa atttatcata
      901 ttttattaaa aataacaacc cagtaaaaaa tgactggtaa aaattcacaa agaaacggaa
      961 agaagcaacc gcagaaaatc aagcttaaaa agagcttttg acctagacca atcgaaaatc
     1021 acaaagtgag cctctgtatc ggttgataca agggctactt ggcatagtgt acattatgtc
     1081 aacaagaatt taatataaca tattttccta atgcattcta actataccac attatcaaaa
     1141 atataaatta tctttactaa ataaaatatt gacaagccta taccttttgt tttatgattt
     1201 tcacaaagaa aacgttttct atatattttt ctgtatcagg aggaaattct atgaaaaaat
     1261 ttactttagg ggtagctttg ttaactattg gggcagttgt tttaccgtca actactatag
     1321 tttatgcttc agaaaattcc caagtggtat cattaaacga aaacaatgct actgaaaatg
     1381 tagttattga gtacactgaa gatggtatgg tcgtaactaa atatgaggat ggttatagtg
     1441 cggaagattt tgcaaattct tcagatatca tgacaagagc tgcagttgca agatggggca
     1501 aaaaggaata tacaaatatt gctgtaacca ctggagtagc tgctaatgct attaatgctg
     1561 ccttttgggc aggagggaaa gctagcactt ctatgtttgg tatcccaggt tgggcaattg
     1621 gtgctttgtt aacaggtgca agttggacta aaaaaggtgc ttctccaggg aatgcagttg
     1681 caaaagaatg ggacaaaaat ggtaatggct ggattggatt ttattaccaa aggggatatg
     1741 atgcagctgg aagagttgta gctactagat attcaacgtt ataagttaag gagtgatgtt
     1801 tttgatatct aaatcattaa aatcattaaa aacatttact aaaaagaatc cgcaaatagc
     1861 tactattcgt atttttatat ttgctatagc tgttgctata attgttaata tgctaagcgg
     1921 agggcaatta tacaaatctg gtttattttt agtgttaatc ttagttgtct tagacataat
     1981 aaagtctaaa aaaaaataaa tcgatacatt ttagaagaat agggttgttt gaatattaca
     2041 aagcaacaat ttcaccttcg gtgaaataag cgaaacttta caaaaagtgg ctagcaaatg
     2101 ctagcctttt tttgtattgt ggagcgtgga ttttgagggg gattcaaggg ggagcttgcg
     2161 ctcctttgac aagcggttat ttgcaccaaa tacggaggta tttggctagc aaatatagag
     2221 cttgccaaac ccttttagtg agctttactc attgtacctt tttaggtaca atggtattgc
     2281 gaacgatacg tccgtaggac gtactgaaag ggtgggactt atgagcgaac aacatcaaaa
     2341 tttggctagc gatcattcta aaaaatatac ctatcgatcc gagccaaaac aaatcagttt
     2401 tcgagtgagc gaatccgaat ttgcaaagct gaagcagtca gctgaagctt tgcaaatgag
     2461 tgtgccggct ttcgtgaaag ccaaggcaca aaacgcgcgt ctggtgacac cgaaagtggc
     2521 gccagacatt gcccaggcaa tcgcgcgcga tttagccaaa gctggaggga atatcaatca
     2581 aattgccaag tggtgcaata cacaccaaca cgacgttgct cctgatgatg ctcaacgttt
     2641 atccgaaaac ctaaaaatca tgcaaaagga gctacaaaag atatggcaac agttaaagta
     2701 agtcgaacca cttcatgtag ccgagcaatc aattacgcag aaccacgagc aaccgtcaaa
     2761 acaggaataa actgtgacat tgattatgcc aaaagtgaaa tgaaacaaat acgcacgctt
     2821 tatggaaaag acgatcgtgt acaagcacac ttattgattc agtcctttcg accaggagaa
     2881 attaccgctg aaaaagccaa tcaactaggg gcagagtatg cgaaaaaaat agcccctaac
     2941 caccaaatcg cgatttacac acatacagac aaagaccata ttcataatca cattgtcatt
     3001 aactccgtta atcttgaaac tgggaaaaaa tttcaagccc atgggcaagc atttttaaac
     3061 aaatgttatg acctaaatga cgagatttgt cttgaacatg acttaacaat cacggaacga
     3121 ggaaagaaaa ccgaaaaacg aaccatgtct gaaattaaat taaaagaaaa aaatgaaccg
     3181 gtttggaaag acgaaattcg gtttgcgatt gatcaaacaa tgaaaaacaa aaaaactcga
     3241 acgtataccc aattttgtga ttcacttaaa acattcggca ttcattgctt gaatcgcgga
     3301 aaaaatttta cttacgaatt ggtccacaaa aagaaaaaag tacgatccaa caaactagga
     3361 aaggattacg aaaaggagac gattttacat gagctggaca gacgagaacg aacctacaat
     3421 caacaacgaa ccaacgagct acgaagagct cgagctagca ttcgcgaaac tgcagaagaa
     3481 gtacgaagag aacaacgaac ttttacgcct gaacaatcgg aaattagacc gactcgaaga
     3541 aaccatgaac aacacgttga acgaggaaca gaccaccaac aagaattatc gctctaaaac
     3601 gttaaaagac atcgaaaacg aaataaagag acaacgtgcc tttcttgcgc cttataccca
     3661 agaaaggata caaactacga tggattcaca agtcaaaaaa ctccaccaag cgctattaga
     3721 ccagcgaaac caagaacaaa aaaaggcttt aattcaacga tcgatggata ttcttgcccc
     3781 cttatgttgc ttagtactaa cattattagc cttttggttg gtatggggag aataaacaga
     3841 catggcattc tatttaccct atctactcat ttctgccagt attttaggaa ttatttggct
     3901 tagctataag gcttatcaaa caagatattc attaaaaggc tctaaaattc gatttaagcg
     3961 atttttattg gtcggggtta tatttgcctt atcaatcgtt ttaagtggtt tattcggcgt
     4021 tttagagggt aataaacgtg tttcaagaag cattttatta ggggatatca ctcaaaagta
     4081 tgaagcagca tgtgataaaa agaaaaaaga gcaagcatta gcacaaaaaa tggaggaatt
     4141 taccgcttgt tatgaggaca tgaacaatat ttttgtggat caagagaaac gtttaacaga
     4201 taaaaacatg aaaaaactca ctcgttttta tcaaaactta ccagaaaaac agcaaaaaga
     4261 ggtacaagaa aaatatgagc aagtaaaaaa agacgtgcaa tattttaaag atacgcagac
     4321 agaagaagct tgttgtaact tatttagcga tacaatccct ttttcaacca gtgaacaaga
     4381 acgaaaagaa cggcaacaat cggtcacata cgaacgttat gaaacactgc ttcagcaagc
     4441 aacaaacata caaaatccaa cgaaaaaaga aacggcatta aattatctag aaagtgtcaa
     4501 ggaatggttg gatcagcaac aacaaaattg aatttgatta gcaatcatgt taaactgaac
     4561 ctgcaaatga tcaaacatta gatacacgaa agccccagag aggtcggatt ctctggggct
     4621 ttttttcagg ttgatgtcgc ctttattgat tttacttctt gtttcggtta ttcaaccaat
     4681 aactgaataa agagacacaa acttctacaa gaagggggca aatgaaccgt tcaaacatta
     4741 gatacacctc cttccagtcg caagactgtc ggataggcga caagttatta taccttacaa
     4801 aataaaatct gtgtggtgtt tttaagtatc ccttattttc gggttgttag ggcttgccct
     4861 gaccgcctgt aaggcgcttt aagaacaaga taaggttttt tacccaagac tgtcttaaaa
     4921 cgacttagac gagctatcag aggcttcccc cacctccgtt actgacttgt ttttagcaaa
     4981 ggagccttta ggcgactgcg cagtacaatg tgagagcata gcgatcacac ttttttagcg
     5041 accgtaggga gcaaggtttt gaattggcag ttttgaaaaa tgcgcgaacc tgttggtaga
     5101 aaaaagaagt ggtttttagg cgggaaattt tgtcaccctc ttttataatc tctttttaaa
     5161 ccttttttta aacctcttta ccgtcggctg tgtccttact ccttcaatgg atacagcgtt
     5221 ttataaacta cattttgtct gcttttaaac tacattttgt ctgcttttaa actacatttt
     5281 gtctgctttt aaactacatt ttgtctgctt ttaaactctt tttttgcact cacgtatgtt
     5341 ataatatgca ttatcacaga caaaacgttg tttataacgt ctgtatccat tgaaggagta
     5401 aggaggaata tctttggcaa atgaaatcgt gaaataccat catgaattaa ataccattcc
     5461 gttgcggaaa tttacaccag ttgaaatgaa tctatttttc tctattgtgt ctagaatgcg
     5521 cgaaaaaggc gataaaacag tccgtcttac ttttgaccaa ctaaaagatt taagtaatta
     5581 taaagcaact gctaataatc gtttcattaa tgatttagaa atgacttatg ataaattaat
     5641 ggatttacgt tttggtaaaa gaagtgctaa tgggctcgat atagatagat tcgttatgtt
     5701 tagtgagttt aaaatacgtg gaactgctaa agatccatat gtagacatac aagtttacga
     5761 aaaagcttta cctttactaa acaatttaga tgagtgggtt cgctattcac tccaacaatt
     5821 taacgaatta caaagtagct atgcaaagac tatgtttcga ttactaaaac aatatcgaac
     5881 taaaggtttt gcttattttt ctaaagagga ttttcatgaa ctattagata ttccaaaaag
     5941 ttactggaac aaccaagcaa acgttgataa tcgtgttata aagcctatac gacaggaatt
     6001 aaccgcaatc ttcaaaggat tatcaatcaa aaagaaatac ggaaaagggc gaggaaaacc
     6061 tgtcgttggc tatcaattta cgtttaaacc agaaatcaaa aaagcagatg attttaataa
     6121 acatgcacca accaaagaag aacaaaataa agcattggct ttagctgata aacaaaaaga
     6181 atacgaagaa cctgctacaa caattaacga aaaaatcaaa cagaagaaac gagaacttga
     6241 actcctccaa caaatcaaac aactagaaaa agagaaagaa gctcttgaaa aacaaacaga
     6301 gtc
//
