LOCUS       NZ_CP066626             6303 bp    DNA     circular CON 20-FEB-2024
DEFINITION  Enterococcus faecium strain Dallas 131_2 plasmid p4, complete
            sequence.
ACCESSION   NZ_CP066626
VERSION     NZ_CP066626.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN17038101
            Assembly: GCF_016415465.1
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  JOURNAL   Unpublished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                   :: 134.0x
            Sequencing Technology :: Illumina NextSeq; Oxford Nanopore MinION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 02/20/2024 02:58:25
            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)                     :: 3,128
            CDSs (total)                      :: 3,037
            Genes (coding)                    :: 2,917
            CDSs (with protein)               :: 2,917
            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)              :: 120
            CDSs (without protein)            :: 120
            Pseudo Genes (ambiguous residues) :: 0 of 120
            Pseudo Genes (frameshifted)       :: 42 of 120
            Pseudo Genes (incomplete)         :: 72 of 120
            Pseudo Genes (internal stop)      :: 30 of 120
            Pseudo Genes (multiple problems)  :: 20 of 120
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP066626.1.
            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 131_2"
                     /isolation_source="rectal swab"
                     /host="Homo sapiens"
                     /db_xref="taxon:1352"
                     /plasmid="p4"
                     /geo_loc_name="USA: Dallas"
                     /collection_date="2015"
     gene            514..1464
                     /locus_tag="JCP79_RS15470"
                     /old_locus_tag="JCP79_15470"
     CDS             514..1464
                     /locus_tag="JCP79_RS15470"
                     /old_locus_tag="JCP79_15470"
                     /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            1485..2018
                     /locus_tag="JCP79_RS15475"
                     /old_locus_tag="JCP79_15475"
     CDS             1485..2018
                     /locus_tag="JCP79_RS15475"
                     /old_locus_tag="JCP79_15475"
                     /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            2034..2204
                     /locus_tag="JCP79_RS15480"
                     /old_locus_tag="JCP79_15480"
     CDS             2034..2204
                     /locus_tag="JCP79_RS15480"
                     /old_locus_tag="JCP79_15480"
                     /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            2654..3187
                     /locus_tag="JCP79_RS15485"
                     /old_locus_tag="JCP79_15485"
     CDS             2654..3187
                     /locus_tag="JCP79_RS15485"
                     /old_locus_tag="JCP79_15485"
                     /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            3199..3402
                     /locus_tag="JCP79_RS15490"
                     /old_locus_tag="JCP79_15490"
     CDS             3199..3402
                     /locus_tag="JCP79_RS15490"
                     /old_locus_tag="JCP79_15490"
                     /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            3724..4104
                     /locus_tag="JCP79_RS15495"
                     /old_locus_tag="JCP79_15495"
     CDS             3724..4104
                     /locus_tag="JCP79_RS15495"
                     /old_locus_tag="JCP79_15495"
                     /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            4086..5000
                     /locus_tag="JCP79_RS15500"
                     /old_locus_tag="JCP79_15500"
     CDS             4086..5000
                     /locus_tag="JCP79_RS15500"
                     /old_locus_tag="JCP79_15500"
                     /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            5245..5934
                     /locus_tag="JCP79_RS15505"
                     /old_locus_tag="JCP79_15505"
     CDS             5245..5934
                     /locus_tag="JCP79_RS15505"
                     /old_locus_tag="JCP79_15505"
                     /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          516..1464
                     /name="rep_cluster_1197"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="84.953"
                     /coverage="99.0"
                     /evalue="0.0"
     Typing          4087..4997
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="94.079"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 tacccaagac tgtcttaaaa cgacttagac gagctatcag aggcttcccc cacctccgtt
       61 actgacttgt ttttagcaaa ggagccttta ggcgactgcg cagtacaatg tgagagcata
      121 gcgatcacac ttttttagcg accgtaggga gcaaggtttt gaattggcag ttttgaaaaa
      181 tgcgcgaacc tgttggtaga aaaaagaagt ggtttttagg cgggaaattt tgtcaccctc
      241 ttttataatc tctttttaaa ccttttttta aacctcttta ccgtcggctg tgtccttact
      301 ccttcaatgg atacagcgtt ttataaacta cattttgtct gcttttaaac tacattttgt
      361 ctgcttttaa actacatttt gtctgctttt aaactacatt ttgtctgctt ttaaactctt
      421 tttttgcact cacgtatgtt ataatatgca ttatcacaga caaaacgttg tttataacgt
      481 ctgtatccat tgaaggagta aggaggaata tctttggcaa atgaaatcgt gaaataccat
      541 catgaattaa ataccattcc gttgcggaaa tttacaccag ttgaaatgaa tctatttttc
      601 tctattgtgt ctagaatgcg cgaaaaaggc gataaaacag tccgtcttac ttttgaccaa
      661 ctaaaagatt taagtaatta taaagcaact gctaataatc gtttcattaa tgatttagaa
      721 atgacttatg ataaattaat ggatttacgt tttggtaaaa gaagtgctaa tgggctcgat
      781 atagatagat tcgttatgtt tagtgagttt aaaatacgtg gaactgctaa agatccatat
      841 gtagacatac aagtttacga aaaagcttta cctttactaa acaatttaga tgagtgggtt
      901 cgctattcac tccaacaatt taacgaatta caaagtagct atgcaaagac tatgtttcga
      961 ttactaaaac aatatcgaac taaaggtttt gcttattttt ctaaagagga ttttcatgaa
     1021 ctattagata ttccaaaaag ttactggaac aaccaagcaa acgttgataa tcgtgttata
     1081 aagcctatac gacaggaatt aaccgcaatc ttcaaaggat tatcaatcaa aaagaaatac
     1141 ggaaaagggc gaggaaaacc tgtcgttggc tatcaattta cgtttaaacc agaaatcaaa
     1201 aaagcagatg attttaataa acatgcacca accaaagaag aacaaaataa agcattggct
     1261 ttagctgata aacaaaaaga atacgaagaa cctgctacaa caattaacga aaaaatcaaa
     1321 cagaagaaac gagaacttga actcctccaa caaatcaaac aactagaaaa agagaaagaa
     1381 gctcttgaaa aacaaacaga gtccgcactt tcgaaaaaag agaaaaaaag tttattatct
     1441 gatttagata atttattcca gtagcaacct aggaggcaac cagtatgcaa ccacaagaaa
     1501 cctttacaat aaaggaattg tcagaacttt ttaagatgag taggcaagca atatcgaaac
     1561 atatccaaaa attagattct tccatgatag ctaaaaatga gcgtggttat aaggttgtat
     1621 tgcgttctgg agtattgcaa cttgctcgca acttaggcaa ccaaatgttg ctagataggt
     1681 tgcacgagta cgaacaagac aacgataaaa atgttaatat accaagcaaa aacgtggtta
     1741 caaacaagtt gctagatcag ttgcgtgaag aaaatgaatt tttacgagaa caacttgccc
     1801 tcagagagca aaataattct catatacaaa aactactcga ccagcaacaa caactcaccc
     1861 tacaagccaa caaacaaatc gaaaaactgc aagaaaaact acagttgact tatacagaag
     1921 aagctccaga gaatgactca acgactcttt ctgaagcaac agaaacaata gacaaacaaa
     1981 ttgatactga aaaaaaatgg tggcaacttt ggaaataact ggagggaaca ttcatgacaa
     2041 gaaaaaatct tctattcggt tctattttac taggaattct aggattcagt ccgatgttat
     2101 tgtcagtgat caataaaggg aataaacatg gtgaattgaa attgaatcca aattattaca
     2161 acagtcctaa cgaagaattg tttgtaaaag aaacagataa ataataaaaa agactgctct
     2221 ttcgagcagc cagttaaaaa ataatgagtg tttattcttg aaaaagcaac gcgcttatga
     2281 agcgctacca aaaatttatc atattttatt aaaaataaca acccagtaaa aaatgactgg
     2341 taaaaattca caaagaaacg gaaagaagca accgcagaaa atcaagctta aaaagagctt
     2401 ttgacctaga ccaatcgaaa atcacaaagt gagcctctgt atcggttgat acaagggcta
     2461 cttggcatag tgtacattat gtcaacaaga atttaatata acatattttc ctaatgcatt
     2521 ctaactatac cacattatca aaaatataaa ttatctttac taaataaaat attgacaagc
     2581 ctataccttt tgttttatga ttttcacaaa gaaaacgttt tctatatatt tttctgtatc
     2641 aggaggaaat tctatgaaaa aatttacttt aggggtagct ttgttaacta ttggggcagt
     2701 tgttttaccg tcaactacta tagtttatgc ttcagaaaat tcccaagtgg tatcattaaa
     2761 cgaaaacaat gctactgaaa atgtagttat tgagtacact gaagatggta tggtcgtaac
     2821 taaatatgag gatggttata gtgcggaaga ttttgcaaat tcttcagata tcatgacaag
     2881 agctgcagtt gcaagatggg gcaaaaagga atatacaaat attgctgtaa ccactggagt
     2941 agctgctaat gctattaatg ctgccttttg ggcaggaggg aaagctagca cttctatgtt
     3001 tggtatccca ggttgggcaa ttggtgcttt gttaacaggt gcaagttgga ctaaaaaagg
     3061 tgcttctcca gggaatgcag ttgcaaaaga atgggacaaa aatggtaatg gctggattgg
     3121 attttattac caaaggggat atgatgcagc tggaagagtt gtagctacta gatattcaac
     3181 gttataagtt aaggagtgat gtttttgata tctaaatcat taaaatcatt aaaaacattt
     3241 actaaaaaga atccgcaaat agctactatt cgtattttta tatttgctat agctgttgct
     3301 ataattgtta atatgctaag cggagggcaa ttatacaaat ctggtttatt tttagtgtta
     3361 atcttagttg tcttagacat aataaagtct aaaaaaaaat aaatcgatac attttagaag
     3421 aatagggttg tttgaatatt acaaagcaac aatttcacct tcggtgaaat aagcgaaact
     3481 ttacaaaaag tggctagcaa atgctagcct ttttttgtat tgtggagcgt ggattttgag
     3541 ggggattcaa gggggagctt gcgctccttt gacaagcggt tatttgcacc aaatacggag
     3601 gtatttggct agcaaatata gagcttgcca aaccctttta gtgagcttta ctcattgtac
     3661 ctttttaggt acaatggtat tgcgaacgat acgtccgtag gacgtactga aagggtggga
     3721 cttatgagcg aacaacatca aaatttggct agcgatcatt ctaaaaaata tacctatcga
     3781 tccgagccaa aacaaatcag ttttcgagtg agcgaatccg aatttgcaaa gctgaagcag
     3841 tcagctgaag ctttgcaaat gagtgtgccg gctttcgtga aagccaaggc acaaaacgcg
     3901 cgtctggtga caccgaaagt ggcgccagac attgcccagg caatcgcgcg cgatttagcc
     3961 aaagctggag ggaatatcaa tcaaattgcc aagtggtgca atacacacca acacgacgtt
     4021 gctcctgatg atgctcaacg tttatccgaa aacctaaaaa tcatgcaaaa ggagctacaa
     4081 aagatatggc aacagttaaa gtaagtcgaa ccacttcatg tagccgagca atcaattacg
     4141 cagaaccacg agcaaccgtc aaaacaggaa taaactgtga cattgattat gccaaaagtg
     4201 aaatgaaaca aatacgcacg ctttatggaa aagacgatcg tgtacaagca cacttattga
     4261 ttcagtcctt tcgaccagga gaaattaccg ctgaaaaagc caatcaacta ggggcagagt
     4321 atgcgaaaaa aatagcccct aaccaccaaa tcgcgattta cacacataca gacaaagacc
     4381 atattcataa tcacattgtc attaactccg ttaatcttga aactgggaaa aaatttcaag
     4441 cccatgggca agcattttta aacaaatgtt atgacctaaa tgacgagatt tgtcttgaac
     4501 atgacttaac aatcacggaa cgaggaaaga aaaccgaaaa acgaaccatg tctgaaatta
     4561 aattaaaaga aaaaaatgaa ccggtttgga aagacgaaat tcggtttgcg attgatcaaa
     4621 caatgaaaaa caaaaaaact cgaacgtata cccaattttg tgattcactt aaaacattcg
     4681 gcattcattg cttgaatcgc ggaaaaaatt ttacttacga attggtccac aaaaagaaaa
     4741 aagtacgatc caacaaacta ggaaaggatt acgaaaagga gacgatttta catgagctgg
     4801 acagacgaga acgaacctac aatcaacaac gaaccaacga gctacgaaga gctcgagcta
     4861 gcattcgcga aactgcagaa gaagtacgaa gagaacaacg aacttttacg cctgaacaat
     4921 cggaaattag accgactcga agaaaccatg aacaacacgt tgaacgagga acagaccacc
     4981 aacaagaatt atcgctctaa aacgttaaaa gacatcgaaa acgaaataaa gagacaacgt
     5041 gcctttcttg cgccttatac ccaagaaagg atacaaacta cgatggattc acaagtcaaa
     5101 aaactccacc aagcgctatt agaccagcga aaccaagaac aaaaaaaggc tttaattcaa
     5161 cgatcgatgg atattcttgc ccccttatgt tgcttagtac taacattatt agccttttgg
     5221 ttggtatggg gagaataaac agacatggca ttctatttac cctatctact catttctgcc
     5281 agtattttag gaattatttg gcttagctat aaggcttatc aaacaagata ttcattaaaa
     5341 ggctctaaaa ttcgatttaa gcgattttta ttggtcgggg ttatatttgc cttatcaatc
     5401 gttttaagtg gtttattcgg cgttttagag ggtaataaac gtgtttcaag aagcatttta
     5461 ttaggggata tcactcaaaa gtatgaagca gcatgtgata aaaagaaaaa agagcaagca
     5521 ttagcacaaa aaatggagga atttaccgct tgttatgagg acatgaacaa tatttttgtg
     5581 gatcaagaga aacgtttaac agataaaaac atgaaaaaac tcactcgttt ttatcaaaac
     5641 ttaccagaaa aacagcaaaa agaggtacaa gaaaaatatg agcaagtaaa aaaagacgtg
     5701 caatatttta aagatacgca gacagaagaa gcttgttgta acttatttag cgatacaatc
     5761 cctttttcaa ccagtgaaca agaacgaaaa gaacggcaac aatcggtcac atacgaacgt
     5821 tatgaaacac tgcttcagca agcaacaaac atacaaaatc caacgaaaaa agaaacggca
     5881 ttaaattatc tagaaagtgt caaggaatgg ttggatcagc aacaacaaaa ttgaatttga
     5941 ttagcaatca tgttaaactg aacctgcaaa tgatcaaaca ttagatacac gaaagcccca
     6001 gagaggtcgg attctctggg gctttttttc aggttgatgt cgcctttatt gattttactt
     6061 cttgtttcgg ttattcaacc aataactgaa taaagagaca caaacttcta caagaagggg
     6121 gcaaatgaac cgttcaaaca ttagatacac ctccttccag tcgcaagact gtcggatagg
     6181 cgacaagtta ttatacctta caaaataaaa tctgtgtggt gtttttaagt atcccttatt
     6241 ttcgggttgt tagggcttgc cctgaccgcc tgtaaggcgc tttaagaaca agataaggtt
     6301 ttt
//
