LOCUS       NZ_CP066477             6303 bp    DNA     circular CON 20-FEB-2024
DEFINITION  Enterococcus faecium strain Dallas 93_2 plasmid p93_2_6.3kb,
            complete sequence.
ACCESSION   NZ_CP066477
VERSION     NZ_CP066477.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN17038088
            Assembly: GCF_016406605.1
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  JOURNAL   Unpublished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                   :: 261.0x
            Sequencing Technology :: Illumina NextSeq; Oxford Nanopore MinION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 02/20/2024 02:57:12
            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)                     :: 3,140
            CDSs (total)                      :: 3,047
            Genes (coding)                    :: 2,906
            CDSs (with protein)               :: 2,906
            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)              :: 141
            CDSs (without protein)            :: 141
            Pseudo Genes (ambiguous residues) :: 0 of 141
            Pseudo Genes (frameshifted)       :: 51 of 141
            Pseudo Genes (incomplete)         :: 81 of 141
            Pseudo Genes (internal stop)      :: 31 of 141
            Pseudo Genes (multiple problems)  :: 18 of 141
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP066477.1.
            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_2"
                     /isolation_source="rectal swab"
                     /host="Homo sapiens"
                     /db_xref="taxon:1352"
                     /plasmid="p93_2_6.3kb"
                     /geo_loc_name="USA: Dallas"
                     /collection_date="2015"
     gene            join(5811..6303,1..197)
                     /locus_tag="JCP72_RS15445"
                     /old_locus_tag="JCP72_15445"
     CDS             join(5811..6303,1..197)
                     /locus_tag="JCP72_RS15445"
                     /old_locus_tag="JCP72_15445"
                     /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            1080..2030
                     /locus_tag="JCP72_RS15455"
                     /old_locus_tag="JCP72_15455"
     CDS             1080..2030
                     /locus_tag="JCP72_RS15455"
                     /old_locus_tag="JCP72_15455"
                     /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            2051..2584
                     /locus_tag="JCP72_RS15460"
                     /old_locus_tag="JCP72_15460"
     CDS             2051..2584
                     /locus_tag="JCP72_RS15460"
                     /old_locus_tag="JCP72_15460"
                     /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            2600..2770
                     /locus_tag="JCP72_RS15465"
                     /old_locus_tag="JCP72_15465"
     CDS             2600..2770
                     /locus_tag="JCP72_RS15465"
                     /old_locus_tag="JCP72_15465"
                     /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            3220..3753
                     /locus_tag="JCP72_RS15470"
                     /old_locus_tag="JCP72_15470"
     CDS             3220..3753
                     /locus_tag="JCP72_RS15470"
                     /old_locus_tag="JCP72_15470"
                     /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            3765..3968
                     /locus_tag="JCP72_RS15475"
                     /old_locus_tag="JCP72_15475"
     CDS             3765..3968
                     /locus_tag="JCP72_RS15475"
                     /old_locus_tag="JCP72_15475"
                     /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            4290..4670
                     /locus_tag="JCP72_RS15480"
                     /old_locus_tag="JCP72_15480"
     CDS             4290..4670
                     /locus_tag="JCP72_RS15480"
                     /old_locus_tag="JCP72_15480"
                     /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            4652..5566
                     /locus_tag="JCP72_RS15485"
                     /old_locus_tag="JCP72_15485"
     CDS             4652..5566
                     /locus_tag="JCP72_RS15485"
                     /old_locus_tag="JCP72_15485"
                     /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          1082..2030
                     /name="rep_cluster_1197"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="84.953"
                     /coverage="99.0"
                     /evalue="0.0"
     Typing          4653..5563
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="94.079"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 gtaacttatt tagcgataca atcccttttt caaccagtga acaagaacga aaagaacggc
       61 aacaatcggt cacatacgaa cgttatgaaa cactgcttca gcaagcaaca aacatacaaa
      121 atccaacgaa aaaagaaacg gcattaaatt atctagaaag tgtcaaggaa tggttggatc
      181 agcaacaaca aaattgaatt tgattagcaa tcatgttaaa ctgaacctgc aaatgatcaa
      241 acattagata cacgaaagcc ccagagaggt cggattctct ggggcttttt ttcaggttga
      301 tgtcgccttt attgatttta cttcttgttt cggttattca accaataact gaataaagag
      361 acacaaactt ctacaagaag ggggcaaatg aaccgttcaa acattagata cacctccttc
      421 cagtcgcaag actgtcggat aggcgacaag ttattatacc ttacaaaata aaatctgtgt
      481 ggtgttttta agtatccctt attttcgggt tgttagggct tgccctgacc gcctgtaagg
      541 cgctttaaga acaagataag gttttttacc caagactgtc ttaaaacgac ttagacgagc
      601 tatcagaggc ttcccccacc tccgttactg acttgttttt agcaaaggag cctttaggcg
      661 actgcgcagt acaatgtgag agcatagcga tcacactttt ttagcgaccg tagggagcaa
      721 ggttttgaat tggcagtttt gaaaaatgcg cgaacctgtt ggtagaaaaa agaagtggtt
      781 tttaggcggg aaattttgtc accctctttt ataatctctt tttaaacctt tttttaaacc
      841 tctttaccgt cggctgtgtc cttactcctt caatggatac agcgttttat aaactacatt
      901 ttgtctgctt ttaaactaca ttttgtctgc ttttaaacta cattttgtct gcttttaaac
      961 tacattttgt ctgcttttaa actctttttt tgcactcacg tatgttataa tatgcattat
     1021 cacagacaaa acgttgttta taacgtctgt atccattgaa ggagtaagga ggaatatctt
     1081 tggcaaatga aatcgtgaaa taccatcatg aattaaatac cattccgttg cggaaattta
     1141 caccagttga aatgaatcta tttttctcta ttgtgtctag aatgcgcgaa aaaggcgata
     1201 aaacagtccg tcttactttt gaccaactaa aagatttaag taattataaa gcaactgcta
     1261 ataatcgttt cattaatgat ttagaaatga cttatgataa attaatggat ttacgttttg
     1321 gtaaaagaag tgctaatggg ctcgatatag atagattcgt tatgtttagt gagtttaaaa
     1381 tacgtggaac tgctaaagat ccatatgtag acatacaagt ttacgaaaaa gctttacctt
     1441 tactaaacaa tttagatgag tgggttcgct attcactcca acaatttaac gaattacaaa
     1501 gtagctatgc aaagactatg tttcgattac taaaacaata tcgaactaaa ggttttgctt
     1561 atttttctaa agaggatttt catgaactat tagatattcc aaaaagttac tggaacaacc
     1621 aagcaaacgt tgataatcgt gttataaagc ctatacgaca ggaattaacc gcaatcttca
     1681 aaggattatc aatcaaaaag aaatacggaa aagggcgagg aaaacctgtc gttggctatc
     1741 aatttacgtt taaaccagaa atcaaaaaag cagatgattt taataaacat gcaccaacca
     1801 aagaagaaca aaataaagca ttggctttag ctgataaaca aaaagaatac gaagaacctg
     1861 ctacaacaat taacgaaaaa atcaaacaga agaaacgaga acttgaactc ctccaacaaa
     1921 tcaaacaact agaaaaagag aaagaagctc ttgaaaaaca aacagagtcc gcactttcga
     1981 aaaaagagaa aaaaagttta ttatctgatt tagataattt attccagtag caacctagga
     2041 ggcaaccagt atgcaaccac aagaaacctt tacaataaag gaattgtcag aactttttaa
     2101 gatgagtagg caagcaatat cgaaacatat ccaaaaatta gattcttcca tgatagctaa
     2161 aaatgagcgt ggttataagg ttgtattgcg ttctggagta ttgcaacttg ctcgcaactt
     2221 aggcaaccaa atgttgctag ataggttgca cgagtacgaa caagacaacg ataaaaatgt
     2281 taatatacca agcaaaaacg tggttacaaa caagttgcta gatcagttgc gtgaagaaaa
     2341 tgaattttta cgagaacaac ttgccctcag agagcaaaat aattctcata tacaaaaact
     2401 actcgaccag caacaacaac tcaccctaca agccaacaaa caaatcgaaa aactgcaaga
     2461 aaaactacag ttgacttata cagaagaagc tccagagaat gactcaacga ctctttctga
     2521 agcaacagaa acaatagaca aacaaattga tactgaaaaa aaatggtggc aactttggaa
     2581 ataactggag ggaacattca tgacaagaaa aaatcttcta ttcggttcta ttttactagg
     2641 aattctagga ttcagtccga tgttattgtc agtgatcaat aaagggaata aacatggtga
     2701 attgaaattg aatccaaatt attacaacag tcctaacgaa gaattgtttg taaaagaaac
     2761 agataaataa taaaaaagac tgctctttcg agcagccagt taaaaaataa tgagtgttta
     2821 ttcttgaaaa agcaacgcgc ttatgaagcg ctaccaaaaa tttatcatat tttattaaaa
     2881 ataacaaccc agtaaaaaat gactggtaaa aattcacaaa gaaacggaaa gaagcaaccg
     2941 cagaaaatca agcttaaaaa gagcttttga cctagaccaa tcgaaaatca caaagtgagc
     3001 ctctgtatcg gttgatacaa gggctacttg gcatagtaca cattatgtca acaagaattt
     3061 aatataacat attttcctaa tgcattctaa ctataccaca ttatcaaaaa tataaattat
     3121 ctttactaaa taaaatattg acaagcctat accttttgtt ttatgatttt cacaaagaaa
     3181 acgttttcta tatatttttc tgtatcagga ggaaattcta tgaaaaaatt tactttaggg
     3241 gtagctttgt taactattgg ggcagttgtt ttaccgtcaa ctactatagt ttatgcttca
     3301 gaaaattccc aagtggtatc attaaacgaa aacaatgcta ctgaaaatgt agttattgag
     3361 tacactgaag atggtatggt cgtaactaaa tatgaggatg gttatagtgc ggaagatttt
     3421 gcaaattctt cagatatcat gacaagagct gcagttgcaa gatggggcaa aaaggaatat
     3481 acaaatattg ctgtaaccac tggagtagct gctaatgcta ttaatgctgc cttttgggca
     3541 ggagggaaag ctagcacttc tatgtttggt atcccaggtt gggcaattgg tgctttgtta
     3601 acaggtgcaa gttggactaa aaaaggtgct tctccaggga atgcagttgc aaaagaatgg
     3661 gacaaaaatg gtaatggctg gattggattt tattaccaaa ggggatatga tgcagctgga
     3721 agagttgtag ctactagata ttcaacgtta taagttaagg agtgatgttt ttgatatcta
     3781 aatcattaaa atcattaaaa acatttacta aaaagaatcc gcaaatagct actattcgta
     3841 tttttatatt tgctatagct gttgctataa ttgttaatat gctaagcgga gggcaattat
     3901 acaaatctgg tttattttta gtgttaatct tagttgtctt agacataata aagtctaaaa
     3961 aaaaataaat cgatacattt tagaagaata gggttgtttg aatattacaa agcaacaatt
     4021 tcaccttcgg tgaaataagc gaaactttac aaaaagtggc tagcaaatgc tagccttttt
     4081 ttgtattgtg gagcgtggat tttgaggggg attcaagggg gagcttgcgc tcctttgaca
     4141 agcggttatt tgcaccaaat acggaggtat ttggctagca aatatagagc ttgccaaacc
     4201 cttttagtga gctttactca ttgtaccttt ttaggtacaa tggtattgcg aacgatacgt
     4261 ccgtaggacg tactgaaagg gtgggactta tgagcgaaca acatcaaaat ttggctagcg
     4321 atcattctaa aaaatatacc tatcgatccg agccaaaaca aatcagtttt cgagtgagcg
     4381 aatccgaatt tgcaaagctg aagcagtcag ctgaagcttt gcaaatgagt gtgccggctt
     4441 tcgtgaaagc caaggcacaa aacgcgcgtc tggtgacacc gaaagtggcg ccagacattg
     4501 cccaggcaat cgcgcgcgat ttagccaaag ctggagggaa tatcaatcaa attgccaagt
     4561 ggtgcaatac acaccaacac gacgttgctc ctgatgatgc tcaacgttta tccgaaaacc
     4621 taaaaatcat gcaaaaggag ctacaaaaga tatggcaaca gttaaagtaa gtcgaaccac
     4681 ttcatgtagc cgagcaatca attacgcaga accacgagca accgtcaaaa caggaataaa
     4741 ctgtgacatt gattatgcca aaagtgaaat gaaacaaata cgcacgcttt atggaaaaga
     4801 cgatcgtgta caagcacact tattgattca gtcctttcga ccaggagaaa ttaccgctga
     4861 aaaagccaat caactagggg cagagtatgc gaaaaaaata gcccctaacc accaaatcgc
     4921 gatttacaca catacagaca aagaccatat tcataatcac attgtcatta actccgttaa
     4981 tcttgaaact gggaaaaaat ttcaagccca tgggcaagca tttttaaaca aatgttatga
     5041 cctaaatgac gagatttgtc ttgaacatga cttaacaatc acggaacgag gaaagaaaac
     5101 cgaaaaacga accatgtctg aaattaaatt aaaagaaaaa aatgaaccgg tttggaaaga
     5161 cgaaattcgg tttgcgattg atcaaacaat gaaaaacaaa aaaactcgaa cgtataccca
     5221 attttgtgat tcacttaaaa cattcggcat tcattgcttg aatcgcggaa aaaattttac
     5281 ttacgaattg gtccacaaaa agaaaaaagt acgatccaac aaactaggaa aggattacga
     5341 aaaggagacg attttacatg agctggacag acgagaacga acctacaatc aacaacgaac
     5401 caacgagcta cgaagagctc gagctagcat tcgcgaaact gcagaagaag tacgaagaga
     5461 acaacgaact tttacgcctg aacaatcgga aattagaccg actcgaagaa accatgaaca
     5521 acacgttgaa cgaggaacag accaccaaca agaattatcg ctctaaaacg ttaaaagaca
     5581 tcgaaaacga aataaagaga caacgtgcct ttcttgcgcc ttatacccaa gaaaggatac
     5641 aaactacgat ggattcacaa gtcaaaaaac tccaccaagc gctattagac cagcgaaacc
     5701 aagaacaaaa aaaggcttta attcaacgat cgatggatat tcttgccccc ttatgttgct
     5761 tagtactaac attattagcc ttttggttgg tatggggaga ataaacagac atggcattct
     5821 atttacccta tctactcatt tctgccagta ttttaggaat tatttggctt agctataagg
     5881 cttatcaaac aagatattca ttaaaaggct ctaaaattcg atttaagcga tttttattgg
     5941 tcggggttat atttgcctta tcaatcgttt taagtggttt attcggcgtt ttagagggta
     6001 ataaacgtgt ttcaagaagc attttattag gggatatcac tcaaaagtat gaagcagcat
     6061 gtgataaaaa gaaaaaagag caagcattag cacaaaaaat ggaggaattt accgcttgtt
     6121 atgaggacat gaacaatatt tttgtggatc aagagaaacg tttaacagat aaaaacatga
     6181 aaaaactcac tcgtttttat caaaacttac cagaaaaaca gcaaaaagag gtacaagaaa
     6241 aatatgagca agtaaaaaaa gacgtgcaat attttaaaga tacgcagaca gaagaagctt
     6301 gtt
//
