LOCUS       NZ_CP066657             6303 bp    DNA     circular CON 20-FEB-2024
DEFINITION  Enterococcus faecium strain Dallas 154_1 plasmid p4, complete
            sequence.
ACCESSION   NZ_CP066657
VERSION     NZ_CP066657.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN17038105
            Assembly: GCF_016415545.1
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  JOURNAL   Unpublished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                   :: 140.0x
            Sequencing Technology :: Illumina NextSeq; Oxford Nanopore MinION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 02/20/2024 02:44:35
            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)                     :: 2,957
            CDSs (total)                      :: 2,864
            Genes (coding)                    :: 2,761
            CDSs (with protein)               :: 2,761
            Genes (RNA)                       :: 93
            rRNAs                             :: 6, 6, 6 (5S, 16S, 23S)
            complete rRNAs                    :: 6, 6, 6 (5S, 16S, 23S)
            tRNAs                             :: 71
            ncRNAs                            :: 4
            Pseudo Genes (total)              :: 103
            CDSs (without protein)            :: 103
            Pseudo Genes (ambiguous residues) :: 0 of 103
            Pseudo Genes (frameshifted)       :: 37 of 103
            Pseudo Genes (incomplete)         :: 62 of 103
            Pseudo Genes (internal stop)      :: 23 of 103
            Pseudo Genes (multiple problems)  :: 16 of 103
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP066657.1.
            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 154_1"
                     /isolation_source="rectal swab"
                     /host="Homo sapiens"
                     /db_xref="taxon:1352"
                     /plasmid="p4"
                     /geo_loc_name="USA: Dallas"
                     /collection_date="2015"
     gene            join(5777..6303,1..7)
                     /locus_tag="JCP65_RS14620"
                     /old_locus_tag="JCP65_14620"
     CDS             join(5777..6303,1..7)
                     /locus_tag="JCP65_RS14620"
                     /old_locus_tag="JCP65_14620"
                     /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            19..222
                     /locus_tag="JCP65_RS14625"
                     /old_locus_tag="JCP65_14625"
     CDS             19..222
                     /locus_tag="JCP65_RS14625"
                     /old_locus_tag="JCP65_14625"
                     /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            544..924
                     /locus_tag="JCP65_RS14630"
                     /old_locus_tag="JCP65_14630"
     CDS             544..924
                     /locus_tag="JCP65_RS14630"
                     /old_locus_tag="JCP65_14630"
                     /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            906..1820
                     /locus_tag="JCP65_RS14635"
                     /old_locus_tag="JCP65_14635"
     CDS             906..1820
                     /locus_tag="JCP65_RS14635"
                     /old_locus_tag="JCP65_14635"
                     /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            2065..2754
                     /locus_tag="JCP65_RS14640"
                     /old_locus_tag="JCP65_14640"
     CDS             2065..2754
                     /locus_tag="JCP65_RS14640"
                     /old_locus_tag="JCP65_14640"
                     /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"
     gene            3637..4587
                     /locus_tag="JCP65_RS14650"
                     /old_locus_tag="JCP65_14650"
     CDS             3637..4587
                     /locus_tag="JCP65_RS14650"
                     /old_locus_tag="JCP65_14650"
                     /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            4608..5141
                     /locus_tag="JCP65_RS14655"
                     /old_locus_tag="JCP65_14655"
     CDS             4608..5141
                     /locus_tag="JCP65_RS14655"
                     /old_locus_tag="JCP65_14655"
                     /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            5157..5327
                     /locus_tag="JCP65_RS14660"
                     /old_locus_tag="JCP65_14660"
     CDS             5157..5327
                     /locus_tag="JCP65_RS14660"
                     /old_locus_tag="JCP65_14660"
                     /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"
     Typing          3639..4587
                     /name="rep_cluster_1197"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="84.953"
                     /coverage="99.0"
                     /evalue="0.0"
     Typing          907..1817
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="94.079"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 gttataagtt aaggagtgat gtttttgata tctaaatcat taaaatcatt aaaaacattt
       61 actaaaaaga atccgcaaat agctactatt cgtattttta tatttgctat agctgttgct
      121 ataattgtta atatgctaag cggagggcaa ttatacaaat ctggtttatt tttagtgtta
      181 atcttagttg tcttagacat aataaagtct aaaaaaaaat aaatcgatac attttagaag
      241 aatagggttg tttgaatatt acaaagcaac aatttcacct tcggtgaaat aagcgaaact
      301 ttacaaaaag tggctagcaa atgctagcct ttttttgtat tgtggagcgt ggattttgag
      361 ggggattcaa gggggagctt gcgctccttt gacaagcggt tatttgcacc aaatacggag
      421 gtatttggct agcaaatata gagcttgcca aaccctttta gtgagcttta ctcattgtac
      481 ctttttaggt acaatggtat tgcgaacgat acgtccgtag gacgtactga aagggtggga
      541 cttatgagcg aacaacatca aaatttggct agcgatcatt ctaaaaaata tacctatcga
      601 tccgagccaa aacaaatcag ttttcgagtg agcgaatccg aatttgcaaa gctgaagcag
      661 tcagctgaag ctttgcaaat gagtgtgccg gctttcgtga aagccaaggc acaaaacgcg
      721 cgtctggtga caccgaaagt ggcgccagac attgcccagg caatcgcgcg cgatttagcc
      781 aaagctggag ggaatatcaa tcaaattgcc aagtggtgca atacacacca acacgacgtt
      841 gctcctgatg atgctcaacg tttatccgaa aacctaaaaa tcatgcaaaa ggagctacaa
      901 aagatatggc aacagttaaa gtaagtcgaa ccacttcatg tagccgagca atcaattacg
      961 cagaaccacg agcaaccgtc aaaacaggaa taaactgtga cattgattat gccaaaagtg
     1021 aaatgaaaca aatacgcacg ctttatggaa aagacgatcg tgtacaagca cacttattga
     1081 ttcagtcctt tcgaccagga gaaattaccg ctgaaaaagc caatcaacta ggggcagagt
     1141 atgcgaaaaa aatagcccct aaccaccaaa tcgcgattta cacacataca gacaaagacc
     1201 atattcataa tcacattgtc attaactccg ttaatcttga aactgggaaa aaatttcaag
     1261 cccatgggca agcattttta aacaaatgtt atgacctaaa tgacgagatt tgtcttgaac
     1321 atgacttaac aatcacggaa cgaggaaaga aaaccgaaaa acgaaccatg tctgaaatta
     1381 aattaaaaga aaaaaatgaa ccggtttgga aagacgaaat tcggtttgcg attgatcaaa
     1441 caatgaaaaa caaaaaaact cgaacgtata cccaattttg tgattcactt aaaacattcg
     1501 gcattcattg cttgaatcgc ggaaaaaatt ttacttacga attggtccac aaaaagaaaa
     1561 aagtacgatc caacaaacta ggaaaggatt acgaaaagga gacgatttta catgagctgg
     1621 acagacgaga acgaacctac aatcaacaac gaaccaacga gctacgaaga gctcgagcta
     1681 gcattcgcga aactgcagaa gaagtacgaa gagaacaacg aacttttacg cctgaacaat
     1741 cggaaattag accgactcga agaaaccatg aacaacacgt tgaacgagga acagaccacc
     1801 aacaagaatt atcgctctaa aacgttaaaa gacatcgaaa acgaaataaa gagacaacgt
     1861 gcctttcttg cgccttatac ccaagaaagg atacaaacta cgatggattc acaagtcaaa
     1921 aaactccacc aagcgctatt agaccagcga aaccaagaac aaaaaaaggc tttaattcaa
     1981 cgatcgatgg atattcttgc ccccttatgt tgcttagtac taacattatt agccttttgg
     2041 ttggtatggg gagaataaac agacatggca ttctatttac cctatctact catttctgcc
     2101 agtattttag gaattatttg gcttagctat aaggcttatc aaacaagata ttcattaaaa
     2161 ggctctaaaa ttcgatttaa gcgattttta ttggtcgggg ttatatttgc cttatcaatc
     2221 gttttaagtg gtttattcgg cgttttagag ggtaataaac gtgtttcaag aagcatttta
     2281 ttaggggata tcactcaaaa gtatgaagca gcatgtgata aaaagaaaaa agagcaagca
     2341 ttagcacaaa aaatggagga atttaccgct tgttatgagg acatgaacaa tatttttgtg
     2401 gatcaagaga aacgtttaac agataaaaac atgaaaaaac tcactcgttt ttatcaaaac
     2461 ttaccagaaa aacagcaaaa agaggtacaa gaaaaatatg agcaagtaaa aaaagacgtg
     2521 caatatttta aagatacgca gacagaagaa gcttgttgta acttatttag cgatacaatc
     2581 cctttttcaa ccagtgaaca agaacgaaaa gaacggcaac aatcggtcac atacgaacgt
     2641 tatgaaacac tgcttcagca agcaacaaac atacaaaatc caacgaaaaa agaaacggca
     2701 ttaaattatc tagaaagtgt caaggaatgg ttggatcagc aacaacaaaa ttgaatttga
     2761 ttagcaatca tgttaaactg aacctgcaaa tgatcaaaca ttagatacac gaaagcccca
     2821 gagaggtcgg attctctggg gctttttttc aggttgatgt cgcctttatt gattttactt
     2881 cttgtttcgg ttattcaacc aataactgaa taaagagaca caaacttcta caagaagggg
     2941 gcaaatgaac cgttcaaaca ttagatacac ctccttccag tcgcaagact gtcggatagg
     3001 cgacaagtta ttatacctta caaaataaaa tctgtgtggt gtttttaagt atcccttatt
     3061 ttcgggttgt tagggcttgc cctgaccgcc tgtaaggcgc tttaagaaca agataaggtt
     3121 ttttacccaa gactgtctta aaacgactta gacgagctat cagaggcttc ccccacctcc
     3181 gttactgact tgtttttagc aaaggagcct ttaggcgact gcgcagtaca atgtgagagc
     3241 atagcgatca cactttttta gcgaccgtag ggagcaaggt tttgaattgg cagttttgaa
     3301 aaatgcgcga acctgttggt agaaaaaaga agtggttttt aggcgggaaa ttttgtcacc
     3361 ctcttttata atctcttttt aaaccttttt ttaaacctct ttaccgtcgg ctgtgtcctt
     3421 actccttcaa tggatacagc gttttataaa ctacattttg tctgctttta aactacattt
     3481 tgtctgcttt taaactacat tttgtctgct tttaaactac attttgtctg cttttaaact
     3541 ctttttttgc actcacgtat gttataatat gcattatcac agacaaaacg ttgtttataa
     3601 cgtctgtatc cattgaagga gtaaggagga atatctttgg caaatgaaat cgtgaaatac
     3661 catcatgaat taaataccat tccgttgcgg aaatttacac cagttgaaat gaatctattt
     3721 ttctctattg tgtctagaat gcgcgaaaaa ggcgataaaa cagtccgtct tacttttgac
     3781 caactaaaag atttaagtaa ttataaagca actgctaata atcgtttcat taatgattta
     3841 gaaatgactt atgataaatt aatggattta cgttttggta aaagaagtgc taatgggctc
     3901 gatatagata gattcgttat gtttagtgag tttaaaatac gtggaactgc taaagatcca
     3961 tatgtagaca tacaagttta cgaaaaagct ttacctttac taaacaattt agatgagtgg
     4021 gttcgctatt cactccaaca atttaacgaa ttacaaagta gctatgcaaa gactatgttt
     4081 cgattactaa aacaatatcg aactaaaggt tttgcttatt tttctaaaga ggattttcat
     4141 gaactattag atattccaaa aagttactgg aacaaccaag caaacgttga taatcgtgtt
     4201 ataaagccta tacgacagga attaaccgca atcttcaaag gattatcaat caaaaagaaa
     4261 tacggaaaag ggcgaggaaa acctgtcgtt ggctatcaat ttacgtttaa accagaaatc
     4321 aaaaaagcag atgattttaa taaacatgca ccaaccaaag aagaacaaaa taaagcattg
     4381 gctttagctg ataaacaaaa agaatacgaa gaacctgcta caacaattaa cgaaaaaatc
     4441 aaacagaaga aacgagaact tgaactcctc caacaaatca aacaactaga aaaagagaaa
     4501 gaagctcttg aaaaacaaac agagtccgca ctttcgaaaa aagagaaaaa aagtttatta
     4561 tctgatttag ataatttatt ccagtagcaa cctaggaggc aaccagtatg caaccacaag
     4621 aaacctttac aataaaggaa ttgtcagaac tttttaagat gagtaggcaa gcaatatcga
     4681 aacatatcca aaaattagat tcttccatga tagctaaaaa tgagcgtggt tataaggttg
     4741 tattgcgttc tggagtattg caacttgctc gcaacttagg caaccaaatg ttgctagata
     4801 ggttgcacga gtacgaacaa gacaacgata aaaatgttaa tataccaagc aaaaacgtgg
     4861 ttacaaacaa gttgctagat cagttgcgtg aagaaaatga atttttacga gaacaacttg
     4921 ccctcagaga gcaaaataat tctcatatac aaaaactact cgaccagcaa caacaactca
     4981 ccctacaagc caacaaacaa atcgaaaaac tgcaagaaaa actacagttg acttatacag
     5041 aagaagctcc agagaatgac tcaacgactc tttctgaagc aacagaaaca atagacaaac
     5101 aaattgatac tgaaaaaaaa tggtggcaac tttggaaata actggaggga acattcatga
     5161 caagaaaaaa tcttctattc ggttctattt tactaggaat tctaggattc agtccgatgt
     5221 tattgtcagt gatcaataaa gggaataaac atggtgaatt gaaattgaat ccaaattatt
     5281 acaacagtcc taacgaagaa ttgtttgtaa aagaaacaga taaataataa aaaagactgc
     5341 tctttcgagc agccagttaa aaaataatga gtgtttattc ttgaaaaagc aacgcgctta
     5401 tgaagcgcta ccaaaaattt atcatatttt attaaaaata acaacccagt aaaaaatgac
     5461 tggtaaaaat tcacaaagaa acggaaagaa gcaaccgcag aaaatcaagc ttaaaaagag
     5521 cttttgacct agaccaatcg aaaatcacaa agtgagcctc tgtatcggtt gatacaaggg
     5581 ctacttggca tagtacacat tatgtcaaca agaatttaat ataacatatt ttcctaatgc
     5641 attctaacta taccacatta tcaaaaatat aaattatctt tactaaataa aatattgaca
     5701 agcctatacc ttttgtttta tgattttcac aaagaaaacg ttttctatat atttttctgt
     5761 atcaggagga aattctatga aaaaatttac tttaggggta gctttgttaa ctattggggc
     5821 agttgtttta ccgtcaacta ctatagttta tgcttcagaa aattcccaag tggtatcatt
     5881 aaacgaaaac aatgctactg aaaatgtagt tattgagtac actgaagatg gtatggtcgt
     5941 aactaaatat gaggatggtt atagtgcgga agattttgca aattcttcag atatcatgac
     6001 aagagctgca gttgcaagat ggggcaaaaa ggaatataca aatattgctg taaccactgg
     6061 agtagctgct aatgctatta atgctgcctt ttgggcagga gggaaagcta gcacttctat
     6121 gtttggtatc ccaggttggg caattggtgc tttgttaaca ggtgcaagtt ggactaaaaa
     6181 aggtgcttct ccagggaatg cagttgcaaa agaatgggac aaaaatggta atggctggat
     6241 tggattttat taccaaaggg gatatgatgc agctggaaga gttgtagcta ctagatattc
     6301 aac
//
