LOCUS       NZ_CP066431             6303 bp    DNA     circular CON 20-FEB-2024
DEFINITION  Enterococcus faecium strain Dallas 57 plasmid p57_6.3kb, complete
            sequence.
ACCESSION   NZ_CP066431
VERSION     NZ_CP066431.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN17038080
            Assembly: GCF_016406565.1
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  JOURNAL   Unpublished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                   :: 132.0x
            Sequencing Technology :: Illumina NextSeq; Oxford Nanopore MinION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 02/20/2024 02:45:54
            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)                     :: 3,132
            CDSs (total)                      :: 3,041
            Genes (coding)                    :: 2,924
            CDSs (with protein)               :: 2,924
            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)              :: 117
            CDSs (without protein)            :: 117
            Pseudo Genes (ambiguous residues) :: 0 of 117
            Pseudo Genes (frameshifted)       :: 41 of 117
            Pseudo Genes (incomplete)         :: 69 of 117
            Pseudo Genes (internal stop)      :: 30 of 117
            Pseudo Genes (multiple problems)  :: 19 of 117
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP066431.1.
            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 57"
                     /isolation_source="rectal swab"
                     /host="Homo sapiens"
                     /db_xref="taxon:1352"
                     /plasmid="p57_6.3kb"
                     /geo_loc_name="USA: Dallas"
                     /collection_date="2015"
     gene            join(5928..6303,1..314)
                     /locus_tag="JCP98_RS15465"
                     /old_locus_tag="JCP98_15465"
     CDS             join(5928..6303,1..314)
                     /locus_tag="JCP98_RS15465"
                     /old_locus_tag="JCP98_15465"
                     /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            1197..2147
                     /locus_tag="JCP98_RS15475"
                     /old_locus_tag="JCP98_15475"
     CDS             1197..2147
                     /locus_tag="JCP98_RS15475"
                     /old_locus_tag="JCP98_15475"
                     /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            2168..2701
                     /locus_tag="JCP98_RS15480"
                     /old_locus_tag="JCP98_15480"
     CDS             2168..2701
                     /locus_tag="JCP98_RS15480"
                     /old_locus_tag="JCP98_15480"
                     /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            2717..2887
                     /locus_tag="JCP98_RS15485"
                     /old_locus_tag="JCP98_15485"
     CDS             2717..2887
                     /locus_tag="JCP98_RS15485"
                     /old_locus_tag="JCP98_15485"
                     /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            3337..3870
                     /locus_tag="JCP98_RS15490"
                     /old_locus_tag="JCP98_15490"
     CDS             3337..3870
                     /locus_tag="JCP98_RS15490"
                     /old_locus_tag="JCP98_15490"
                     /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            complement(3872..4063)
                     /locus_tag="JCP98_RS15495"
                     /old_locus_tag="JCP98_15495"
     CDS             complement(3872..4063)
                     /locus_tag="JCP98_RS15495"
                     /old_locus_tag="JCP98_15495"
                     /inference="COORDINATES: ab initio prediction:GeneMarkS-2+"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GeneMarkS-2+."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_189660793.1"
                     /translation="MSKTTKINTKNKPDLYNCPPLSILTIIATAIANIKIRIVAICGFF
                     LVNVFNDFNDLDIKNITP"
                     /name="hypothetical protein"
     gene            4407..4787
                     /locus_tag="JCP98_RS15500"
                     /old_locus_tag="JCP98_15500"
     CDS             4407..4787
                     /locus_tag="JCP98_RS15500"
                     /old_locus_tag="JCP98_15500"
                     /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            4769..5683
                     /locus_tag="JCP98_RS15505"
                     /old_locus_tag="JCP98_15505"
     CDS             4769..5683
                     /locus_tag="JCP98_RS15505"
                     /old_locus_tag="JCP98_15505"
                     /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          1199..2147
                     /name="rep_cluster_1197"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="84.953"
                     /coverage="99.0"
                     /evalue="0.0"
     Typing          4770..5680
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="94.079"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 tcactcgttt ttatcaaaac ttaccagaaa aacagcaaaa agaggtacaa gaaaaatatg
       61 agcaagtaaa aaaagacgtg caatatttta aagatacgca gacagaagaa gcttgttgta
      121 acttatttag cgatacaatc cctttttcaa ccagtgaaca agaacgaaaa gaacggcaac
      181 aatcggtcac atacgaacgt tatgaaacac tgcttcagca agcaacaaac atacaaaatc
      241 caacgaaaaa agaaacggca ttaaattatc tagaaagtgt caaggaatgg ttggatcagc
      301 aacaacaaaa ttgaatttga ttagcaatca tgttaaactg aacctgcaaa tgatcaaaca
      361 ttagatacac gaaagcccca gagaggtcgg attctctggg gctttttttc aggttgatgt
      421 cgcctttatt gattttactt cttgtttcgg ttattcaacc aataactgaa taaagagaca
      481 caaacttcta caagaagggg gcaaatgaac cgttcaaaca ttagatacac ctccttccag
      541 tcgcaagact gtcggatagg cgacaagtta ttatacctta caaaataaaa tctgtgtggt
      601 gtttttaagt atcccttatt ttcgggttgt tagggcttgc cctgaccgcc tgtaaggcgc
      661 tttaagaaca agataaggtt ttttacccaa gactgtctta aaacgactta gacgagctat
      721 cagaggcttc ccccacctcc gttactgact tgtttttagc aaaggagcct ttaggcgact
      781 gcgcagtaca atgtgagagc atagcgatca cactttttta gcgaccgtag ggagcaaggt
      841 tttgaattgg cagttttgaa aaatgcgcga acctgttggt agaaaaaaga agtggttttt
      901 aggcgggaaa ttttgtcacc ctcttttata atctcttttt aaaccttttt ttaaacctct
      961 ttaccgtcgg ctgtgtcctt actccttcaa tggatacagc gttttataaa ctacattttg
     1021 tctgctttta aactacattt tgtctgcttt taaactacat tttgtctgct tttaaactac
     1081 attttgtctg cttttaaact ctttttttgc actcacgtat gttataatat gcattatcac
     1141 agacaaaacg ttgtttataa cgtctgtatc cattgaagga gtaaggagga atatctttgg
     1201 caaatgaaat cgtgaaatac catcatgaat taaataccat tccgttgcgg aaatttacac
     1261 cagttgaaat gaatctattt ttctctattg tgtctagaat gcgcgaaaaa ggcgataaaa
     1321 cagtccgtct tacttttgac caactaaaag atttaagtaa ttataaagca actgctaata
     1381 atcgtttcat taatgattta gaaatgactt atgataaatt aatggattta cgttttggta
     1441 aaagaagtgc taatgggctc gatatagata gattcgttat gtttagtgag tttaaaatac
     1501 gtggaactgc taaagatcca tatgtagaca tacaagttta cgaaaaagct ttacctttac
     1561 taaacaattt agatgagtgg gttcgctatt cactccaaca atttaacgaa ttacaaagta
     1621 gctatgcaaa gactatgttt cgattactaa aacaatatcg aactaaaggt tttgcttatt
     1681 tttctaaaga ggattttcat gaactattag atattccaaa aagttactgg aacaaccaag
     1741 caaacgttga taatcgtgtt ataaagccta tacgacagga attaaccgca atcttcaaag
     1801 gattatcaat caaaaagaaa tacggaaaag ggcgaggaaa acctgtcgtt ggctatcaat
     1861 ttacgtttaa accagaaatc aaaaaagcag atgattttaa taaacatgca ccaaccaaag
     1921 aagaacaaaa taaagcattg gctttagctg ataaacaaaa agaatacgaa gaacctgcta
     1981 caacaattaa cgaaaaaatc aaacagaaga aacgagaact tgaactcctc caacaaatca
     2041 aacaactaga aaaagagaaa gaagctcttg aaaaacaaac agagtccgca ctttcgaaaa
     2101 aagagaaaaa aagtttatta tctgatttag ataatttatt ccagtagcaa cctaggaggc
     2161 aaccagtatg caaccacaag aaacctttac aataaaggaa ttgtcagaac tttttaagat
     2221 gagtaggcaa gcaatatcga aacatatcca aaaattagat tcttccatga tagctaaaaa
     2281 tgagcgtggt tataaggttg tattgcgttc tggagtattg caacttgctc gcaacttagg
     2341 caaccaaatg ttgctagata ggttgcacga gtacgaacaa gacaacgata aaaatgttaa
     2401 tataccaagc aaaaacgtgg ttacaaacaa gttgctagat cagttgcgtg aagaaaatga
     2461 atttttacga gaacaacttg ccctcagaga gcaaaataat tctcatatac aaaaactact
     2521 cgaccagcaa caacaactca ccctacaagc caacaaacaa atcgaaaaac tgcaagaaaa
     2581 actacagttg acttatacag aagaagctcc agagaatgac tcaacgactc tttctgaagc
     2641 aacagaaaca atagacaaac aaattgatac tgaaaaaaaa tggtggcaac tttggaaata
     2701 actggaggga acattcatga caagaaaaaa tcttctattc ggttctattt tactaggaat
     2761 tctaggattc agtccgatgt tattgtcagt gatcaataaa gggaataaac atggtgaatt
     2821 gaaattgaat ccaaattatt acaacagtcc taacgaagaa ttgtttgtaa aagaaacaga
     2881 taaataataa aaaagactgc tctttcgagc agccagttaa aaaataatga gtgtttattc
     2941 ttgaaaaagc aacgcgctta tgaagcgcta ccaaaaattt atcatatttt attaaaaata
     3001 acaacccagt aaaaaatgac tggtaaaaat tcacaaagaa acggaaagaa gcaaccgcag
     3061 aaaatcaagc ttaaaaagag cttttgacct agaccaatcg aaaatcacaa agtgagcctc
     3121 tgtatcggtt gatacaaggg ctacttggca tagtgtacat tatgtcaaca agaatttaat
     3181 ataacatatt ttcctaatgc attctaacta taccacatta tcaaaaatat aaattatctt
     3241 tactaaataa aatattgaca agcctatacc ttttgtttta tgattttcac aaagaaaacg
     3301 ttttctatat atttttctgt atcaggagga aattctatga aaaaatttac tttaggggta
     3361 gctttgttaa ctattggggc agttgtttta ccgtcaacta ctatagttta tgcttcagaa
     3421 aattcccaag tggtatcatt aaacgaaaac aatgctactg aaaatgtagt tattgagtac
     3481 actgaagatg gtatggtcgt aactaaatat gaggatggtt atagtgcgga agattttgca
     3541 aattcttcag atatcatgac aagagctgca gttgcaagat ggggcaaaaa ggaatataca
     3601 aatattgctg taaccactgg agtagctgct aatgctatta atgctgcctt ttgggcagga
     3661 gggaaagcta gcacttctat gtttggtatc ccaggttggg caattggtgc tttgttaaca
     3721 ggtgcaagtt ggactaaaaa aggtgcttct ccagggaatg cagttgcaaa agaatgggac
     3781 aaaaatggta atggctggat tggattttat taccaaaggg gatatgatgc agctggaaga
     3841 gttgtagcta ctagatattc aacgttataa gttaaggagt gatgtttttg atatctaaat
     3901 cattaaaatc attaaaaaca tttactaaaa agaatccgca aatagctact attcgtattt
     3961 ttatatttgc tatagctgtt gctataattg ttaatatgct aagcggaggg caattataca
     4021 aatctggttt atttttagtg ttaatcttag ttgtcttaga cataataaag tctaaaaaaa
     4081 aataaatcga tacattttag aagaataggg ttgtttgaat attacaaagc aacaatttca
     4141 ccttcggtga aataagcgaa actttacaaa aagtggctag caaatgctag cctttttttg
     4201 tattgtggag cgtggatttt gagggggatt caagggggag cttgcgctcc tttgacaagc
     4261 ggttatttgc accaaatacg gaggtatttg gctagcaaat atagagcttg ccaaaccctt
     4321 ttagtgagct ttactcattg taccttttta ggtacaatgg tattgcgaac gatacgtccg
     4381 taggacgtac tgaaagggtg ggacttatga gcgaacaaca tcaaaatttg gctagcgatc
     4441 attctaaaaa atatacctat cgatccgagc caaaacaaat cagttttcga gtgagcgaat
     4501 ccgaatttgc aaagctgaag cagtcagctg aagctttgca aatgagtgtg ccggctttcg
     4561 tgaaagccaa ggcacaaaac gcgcgtctgg tgacaccgaa agtggcgcca gacattgccc
     4621 aggcaatcgc gcgcgattta gccaaagctg gagggaatat caatcaaatt gccaagtggt
     4681 gcaatacaca ccaacacgac gttgctcctg atgatgctca acgtttatcc gaaaacctaa
     4741 aaatcatgca aaaggagcta caaaagatat ggcaacagtt aaagtaagtc gaaccacttc
     4801 atgtagccga gcaatcaatt acgcagaacc acgagcaacc gtcaaaacag gaataaactg
     4861 tgacattgat tatgccaaaa gtgaaatgaa acaaatacgc acgctttatg gaaaagacga
     4921 tcgtgtacaa gcacacttat tgattcagtc ctttcgacca ggagaaatta ccgctgaaaa
     4981 agccaatcaa ctaggggcag agtatgcgaa aaaaatagcc cctaaccacc aaatcgcgat
     5041 ttacacacat acagacaaag accatattca taatcacatt gtcattaact ccgttaatct
     5101 tgaaactggg aaaaaatttc aagcccatgg gcaagcattt ttaaacaaat gttatgacct
     5161 aaatgacgag atttgtcttg aacatgactt aacaatcacg gaacgaggaa agaaaaccga
     5221 aaaacgaacc atgtctgaaa ttaaattaaa agaaaaaaat gaaccggttt ggaaagacga
     5281 aattcggttt gcgattgatc aaacaatgaa aaacaaaaaa actcgaacgt atacccaatt
     5341 ttgtgattca cttaaaacat tcggcattca ttgcttgaat cgcggaaaaa attttactta
     5401 cgaattggtc cacaaaaaga aaaaagtacg atccaacaaa ctaggaaagg attacgaaaa
     5461 ggagacgatt ttacatgagc tggacagacg agaacgaacc tacaatcaac aacgaaccaa
     5521 cgagctacga agagctcgag ctagcattcg cgaaactgca gaagaagtac gaagagaaca
     5581 acgaactttt acgcctgaac aatcggaaat tagaccgact cgaagaaacc atgaacaaca
     5641 cgttgaacga ggaacagacc accaacaaga attatcgctc taaaacgtta aaagacatcg
     5701 aaaacgaaat aaagagacaa cgtgcctttc ttgcgcctta tacccaagaa aggatacaaa
     5761 ctacgatgga ttcacaagtc aaaaaactcc accaagcgct attagaccag cgaaaccaag
     5821 aacaaaaaaa ggctttaatt caacgatcga tggatattct tgccccctta tgttgcttag
     5881 tactaacatt attagccttt tggttggtat ggggagaata aacagacatg gcattctatt
     5941 taccctatct actcatttct gccagtattt taggaattat ttggcttagc tataaggctt
     6001 atcaaacaag atattcatta aaaggctcta aaattcgatt taagcgattt ttattggtcg
     6061 gggttatatt tgccttatca atcgttttaa gtggtttatt cggcgtttta gagggtaata
     6121 aacgtgtttc aagaagcatt ttattagggg atatcactca aaagtatgaa gcagcatgtg
     6181 ataaaaagaa aaaagagcaa gcattagcac aaaaaatgga ggaatttacc gcttgttatg
     6241 aggacatgaa caatattttt gtggatcaag agaaacgttt aacagataaa aacatgaaaa
     6301 aac
//
