LOCUS       NZ_CP066413             6303 bp    DNA     circular CON 20-FEB-2024
DEFINITION  Enterococcus faecium strain Dallas 53_2 plasmid p53_2_6.3kb,
            complete sequence.
ACCESSION   NZ_CP066413
VERSION     NZ_CP066413.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN17038077
            Assembly: GCF_016406545.1
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  JOURNAL   Unpublished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 (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                   :: 147.0x
            Sequencing Technology :: Illumina NextSeq; Oxford Nanopore MinION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 02/20/2024 02:46:55
            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)                     :: 3,126
            CDSs (total)                      :: 3,035
            Genes (coding)                    :: 2,920
            CDSs (with protein)               :: 2,920
            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)              :: 115
            CDSs (without protein)            :: 115
            Pseudo Genes (ambiguous residues) :: 0 of 115
            Pseudo Genes (frameshifted)       :: 42 of 115
            Pseudo Genes (incomplete)         :: 67 of 115
            Pseudo Genes (internal stop)      :: 30 of 115
            Pseudo Genes (multiple problems)  :: 20 of 115
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP066413.1.
            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 53_2"
                     /isolation_source="rectal swab"
                     /host="Homo sapiens"
                     /db_xref="taxon:1352"
                     /plasmid="p53_2_6.3kb"
                     /geo_loc_name="USA: Dallas"
                     /collection_date="2015"
     gene            join(5918..6303,1..304)
                     /locus_tag="JCP94_RS15490"
                     /old_locus_tag="JCP94_15490"
     CDS             join(5918..6303,1..304)
                     /locus_tag="JCP94_RS15490"
                     /old_locus_tag="JCP94_15490"
                     /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            1187..2137
                     /locus_tag="JCP94_RS15500"
                     /old_locus_tag="JCP94_15500"
     CDS             1187..2137
                     /locus_tag="JCP94_RS15500"
                     /old_locus_tag="JCP94_15500"
                     /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            2158..2691
                     /locus_tag="JCP94_RS15505"
                     /old_locus_tag="JCP94_15505"
     CDS             2158..2691
                     /locus_tag="JCP94_RS15505"
                     /old_locus_tag="JCP94_15505"
                     /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            2707..2877
                     /locus_tag="JCP94_RS15510"
                     /old_locus_tag="JCP94_15510"
     CDS             2707..2877
                     /locus_tag="JCP94_RS15510"
                     /old_locus_tag="JCP94_15510"
                     /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            3327..3860
                     /locus_tag="JCP94_RS15515"
                     /old_locus_tag="JCP94_15515"
     CDS             3327..3860
                     /locus_tag="JCP94_RS15515"
                     /old_locus_tag="JCP94_15515"
                     /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            3872..4075
                     /locus_tag="JCP94_RS15520"
                     /old_locus_tag="JCP94_15520"
     CDS             3872..4075
                     /locus_tag="JCP94_RS15520"
                     /old_locus_tag="JCP94_15520"
                     /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            4397..4777
                     /locus_tag="JCP94_RS15525"
                     /old_locus_tag="JCP94_15525"
     CDS             4397..4777
                     /locus_tag="JCP94_RS15525"
                     /old_locus_tag="JCP94_15525"
                     /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            4759..5673
                     /locus_tag="JCP94_RS15530"
                     /old_locus_tag="JCP94_15530"
     CDS             4759..5673
                     /locus_tag="JCP94_RS15530"
                     /old_locus_tag="JCP94_15530"
                     /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"
     Typing          1189..2137
                     /name="rep_cluster_1197"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="84.953"
                     /coverage="99.0"
                     /evalue="0.0"
     Typing          4760..5670
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="94.079"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 ttatcaaaac ttaccagaaa aacagcaaaa agaggtacaa gaaaaatatg agcaagtaaa
       61 aaaagacgtg caatatttta aagatacgca gacagaagaa gcttgttgta acttatttag
      121 cgatacaatc cctttttcaa ccagtgaaca agaacgaaaa gaacggcaac aatcggtcac
      181 atacgaacgt tatgaaacac tgcttcagca agcaacaaac atacaaaatc caacgaaaaa
      241 agaaacggca ttaaattatc tagaaagtgt caaggaatgg ttggatcagc aacaacaaaa
      301 ttgaatttga ttagcaatca tgttaaactg aacctgcaaa tgatcaaaca ttagatacac
      361 gaaagcccca gagaggtcgg attctctggg gctttttttc aggttgatgt cgcctttatt
      421 gattttactt cttgtttcgg ttattcaacc aataactgaa taaagagaca caaacttcta
      481 caagaagggg gcaaatgaac cgttcaaaca ttagatacac ctccttccag tcgcaagact
      541 gtcggatagg cgacaagtta ttatacctta caaaataaaa tctgtgtggt gtttttaagt
      601 atcccttatt ttcgggttgt tagggcttgc cctgaccgcc tgtaaggcgc tttaagaaca
      661 agataaggtt ttttacccaa gactgtctta aaacgactta gacgagctat cagaggcttc
      721 ccccacctcc gttactgact tgtttttagc aaaggagcct ttaggcgact gcgcagtaca
      781 atgtgagagc atagcgatca cactttttta gcgaccgtag ggagcaaggt tttgaattgg
      841 cagttttgaa aaatgcgcga acctgttggt agaaaaaaga agtggttttt aggcgggaaa
      901 ttttgtcacc ctcttttata atctcttttt aaaccttttt ttaaacctct ttaccgtcgg
      961 ctgtgtcctt actccttcaa tggatacagc gttttataaa ctacattttg tctgctttta
     1021 aactacattt tgtctgcttt taaactacat tttgtctgct tttaaactac attttgtctg
     1081 cttttaaact ctttttttgc actcacgtat gttataatat gcattatcac agacaaaacg
     1141 ttgtttataa cgtctgtatc cattgaagga gtaaggagga atatctttgg caaatgaaat
     1201 cgtgaaatac catcatgaat taaataccat tccgttgcgg aaatttacac cagttgaaat
     1261 gaatctattt ttctctattg tgtctagaat gcgcgaaaaa ggcgataaaa cagtccgtct
     1321 tacttttgac caactaaaag atttaagtaa ttataaagca actgctaata atcgtttcat
     1381 taatgattta gaaatgactt atgataaatt aatggattta cgttttggta aaagaagtgc
     1441 taatgggctc gatatagata gattcgttat gtttagtgag tttaaaatac gtggaactgc
     1501 taaagatcca tatgtagaca tacaagttta cgaaaaagct ttacctttac taaacaattt
     1561 agatgagtgg gttcgctatt cactccaaca atttaacgaa ttacaaagta gctatgcaaa
     1621 gactatgttt cgattactaa aacaatatcg aactaaaggt tttgcttatt tttctaaaga
     1681 ggattttcat gaactattag atattccaaa aagttactgg aacaaccaag caaacgttga
     1741 taatcgtgtt ataaagccta tacgacagga attaaccgca atcttcaaag gattatcaat
     1801 caaaaagaaa tacggaaaag ggcgaggaaa acctgtcgtt ggctatcaat ttacgtttaa
     1861 accagaaatc aaaaaagcag atgattttaa taaacatgca ccaaccaaag aagaacaaaa
     1921 taaagcattg gctttagctg ataaacaaaa agaatacgaa gaacctgcta caacaattaa
     1981 cgaaaaaatc aaacagaaga aacgagaact tgaactcctc caacaaatca aacaactaga
     2041 aaaagagaaa gaagctcttg aaaaacaaac agagtccgca ctttcgaaaa aagagaaaaa
     2101 aagtttatta tctgatttag ataatttatt ccagtagcaa cctaggaggc aaccagtatg
     2161 caaccacaag aaacctttac aataaaggaa ttgtcagaac tttttaagat gagtaggcaa
     2221 gcaatatcga aacatatcca aaaattagat tcttccatga tagctaaaaa tgagcgtggt
     2281 tataaggttg tattgcgttc tggagtattg caacttgctc gcaacttagg caaccaaatg
     2341 ttgctagata ggttgcacga gtacgaacaa gacaacgata aaaatgttaa tataccaagc
     2401 aaaaacgtgg ttacaaacaa gttgctagat cagttgcgtg aagaaaatga atttttacga
     2461 gaacaacttg ccctcagaga gcaaaataat tctcatatac aaaaactact cgaccagcaa
     2521 caacaactca ccctacaagc caacaaacaa atcgaaaaac tgcaagaaaa actacagttg
     2581 acttatacag aagaagctcc agagaatgac tcaacgactc tttctgaagc aacagaaaca
     2641 atagacaaac aaattgatac tgaaaaaaaa tggtggcaac tttggaaata actggaggga
     2701 acattcatga caagaaaaaa tcttctattc ggttctattt tactaggaat tctaggattc
     2761 agtccgatgt tattgtcagt gatcaataaa gggaataaac atggtgaatt gaaattgaat
     2821 ccaaattatt acaacagtcc taacgaagaa ttgtttgtaa aagaaacaga taaataataa
     2881 aaaagactgc tctttcgagc agccagttaa aaaataatga gtgtttattc ttgaaaaagc
     2941 aacgcgctta tgaagcgcta ccaaaaattt atcatatttt attaaaaata acaacccagt
     3001 aaaaaatgac tggtaaaaat tcacaaagaa acggaaagaa gcaaccgcag aaaatcaagc
     3061 ttaaaaagag cttttgacct agaccaatcg aaaatcacaa agtgagcctc tgtatcggtt
     3121 gatacaaggg ctacttggca tagtgtacat tatgtcaaca agaatttaat ataacatatt
     3181 ttcctaatgc attctaacta taccacatta tcaaaaatat aaattatctt tactaaataa
     3241 aatattgaca agcctatacc ttttgtttta tgattttcac aaagaaaacg ttttctatat
     3301 atttttctgt atcaggagga aattctatga aaaaatttac tttaggggta gctttgttaa
     3361 ctattggggc agttgtttta ccgtcaacta ctatagttta tgcttcagaa aattcccaag
     3421 tggtatcatt aaacgaaaac aatgctactg aaaatgtagt tattgagtac actgaagatg
     3481 gtatggtcgt aactaaatat gaggatggtt atagtgcgga agattttgca aattcttcag
     3541 atatcatgac aagagctgca gttgcaagat ggggcaaaaa ggaatataca aatattgctg
     3601 taaccactgg agtagctgct aatgctatta atgctgcctt ttgggcagga gggaaagcta
     3661 gcacttctat gtttggtatc ccaggttggg caattggtgc tttgttaaca ggtgcaagtt
     3721 ggactaaaaa aggtgcttct ccagggaatg cagttgcaaa agaatgggac aaaaatggta
     3781 atggctggat tggattttat taccaaaggg gatatgatgc agctggaaga gttgtagcta
     3841 ctagatattc aacgttataa gttaaggagt gatgtttttg atatctaaat cattaaaatc
     3901 attaaaaaca tttactaaaa agaatccgca aatagctact attcgtattt ttatatttgc
     3961 tatagctgtt gctataattg ttaatatgct aagcggaggg caattataca aatctggttt
     4021 atttttagtg ttaatcttag ttgtcttaga cataataaag tctaaaaaaa aataaatcga
     4081 tacattttag aagaataggg ttgtttgaat attacaaagc aacaatttca ccttcggtga
     4141 aataagcgaa actttacaaa aagtggctag caaatgctag cctttttttg tattgtggag
     4201 cgtggatttt gagggggatt caagggggag cttgcgctcc tttgacaagc ggttatttgc
     4261 accaaatacg gaggtatttg gctagcaaat atagagcttg ccaaaccctt ttagtgagct
     4321 ttactcattg taccttttta ggtacaatgg tattgcgaac gatacgtccg taggacgtac
     4381 tgaaagggtg ggacttatga gcgaacaaca tcaaaatttg gctagcgatc attctaaaaa
     4441 atatacctat cgatccgagc caaaacaaat cagttttcga gtgagcgaat ccgaatttgc
     4501 aaagctgaag cagtcagctg aagctttgca aatgagtgtg ccggctttcg tgaaagccaa
     4561 ggcacaaaac gcgcgtctgg tgacaccgaa agtggcgcca gacattgccc aggcaatcgc
     4621 gcgcgattta gccaaagctg gagggaatat caatcaaatt gccaagtggt gcaatacaca
     4681 ccaacacgac gttgctcctg atgatgctca acgtttatcc gaaaacctaa aaatcatgca
     4741 aaaggagcta caaaagatat ggcaacagtt aaagtaagtc gaaccacttc atgtagccga
     4801 gcaatcaatt acgcagaacc acgagcaacc gtcaaaacag gaataaactg tgacattgat
     4861 tatgccaaaa gtgaaatgaa acaaatacgc acgctttatg gaaaagacga tcgtgtacaa
     4921 gcacacttat tgattcagtc ctttcgacca ggagaaatta ccgctgaaaa agccaatcaa
     4981 ctaggggcag agtatgcgaa aaaaatagcc cctaaccacc aaatcgcgat ttacacacat
     5041 acagacaaag accatattca taatcacatt gtcattaact ccgttaatct tgaaactggg
     5101 aaaaaatttc aagcccatgg gcaagcattt ttaaacaaat gttatgacct aaatgacgag
     5161 atttgtcttg aacatgactt aacaatcacg gaacgaggaa agaaaaccga aaaacgaacc
     5221 atgtctgaaa ttaaattaaa agaaaaaaat gaaccggttt ggaaagacga aattcggttt
     5281 gcgattgatc aaacaatgaa aaacaaaaaa actcgaacgt atacccaatt ttgtgattca
     5341 cttaaaacat tcggcattca ttgcttgaat cgcggaaaaa attttactta cgaattggtc
     5401 cacaaaaaga aaaaagtacg atccaacaaa ctaggaaagg attacgaaaa ggagacgatt
     5461 ttacatgagc tggacagacg agaacgaacc tacaatcaac aacgaaccaa cgagctacga
     5521 agagctcgag ctagcattcg cgaaactgca gaagaagtac gaagagaaca acgaactttt
     5581 acgcctgaac aatcggaaat tagaccgact cgaagaaacc atgaacaaca cgttgaacga
     5641 ggaacagacc accaacaaga attatcgctc taaaacgtta aaagacatcg aaaacgaaat
     5701 aaagagacaa cgtgcctttc ttgcgcctta tacccaagaa aggatacaaa ctacgatgga
     5761 ttcacaagtc aaaaaactcc accaagcgct attagaccag cgaaaccaag aacaaaaaaa
     5821 ggctttaatt caacgatcga tggatattct tgccccctta tgttgcttag tactaacatt
     5881 attagccttt tggttggtat ggggagaata aacagacatg gcattctatt taccctatct
     5941 actcatttct gccagtattt taggaattat ttggcttagc tataaggctt atcaaacaag
     6001 atattcatta aaaggctcta aaattcgatt taagcgattt ttattggtcg gggttatatt
     6061 tgccttatca atcgttttaa gtggtttatt cggcgtttta gagggtaata aacgtgtttc
     6121 aagaagcatt ttattagggg atatcactca aaagtatgaa gcagcatgtg ataaaaagaa
     6181 aaaagagcaa gcattagcac aaaaaatgga ggaatttacc gcttgttatg aggacatgaa
     6241 caatattttt gtggatcaag agaaacgttt aacagataaa aacatgaaaa aactcactcg
     6301 ttt
//
