LOCUS       NZ_CP066618             6303 bp    DNA     circular CON 20-FEB-2024
DEFINITION  Enterococcus faecium strain Dallas 124_3 plasmid p124_3_6.3kb,
            complete sequence.
ACCESSION   NZ_CP066618
VERSION     NZ_CP066618.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN17038100
            Assembly: GCF_016415365.1
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  JOURNAL   Unpublished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                   :: 299.0x
            Sequencing Technology :: Illumina NextSeq; Oxford Nanopore MinION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 02/20/2024 02:58:57
            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)                     :: 3,103
            CDSs (total)                      :: 3,012
            Genes (coding)                    :: 2,889
            CDSs (with protein)               :: 2,889
            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)              :: 123
            CDSs (without protein)            :: 123
            Pseudo Genes (ambiguous residues) :: 0 of 123
            Pseudo Genes (frameshifted)       :: 41 of 123
            Pseudo Genes (incomplete)         :: 74 of 123
            Pseudo Genes (internal stop)      :: 32 of 123
            Pseudo Genes (multiple problems)  :: 20 of 123
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP066618.1.
            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 124_3"
                     /isolation_source="rectal swab"
                     /host="Homo sapiens"
                     /db_xref="taxon:1352"
                     /plasmid="p124_3_6.3kb"
                     /geo_loc_name="USA: Dallas"
                     /collection_date="2015"
     gene            join(6196..6303,1..426)
                     /locus_tag="JCP92_RS15320"
                     /old_locus_tag="JCP92_15320"
     CDS             join(6196..6303,1..426)
                     /locus_tag="JCP92_RS15320"
                     /old_locus_tag="JCP92_15320"
                     /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            442..612
                     /locus_tag="JCP92_RS15325"
                     /old_locus_tag="JCP92_15325"
     CDS             442..612
                     /locus_tag="JCP92_RS15325"
                     /old_locus_tag="JCP92_15325"
                     /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            1062..1595
                     /locus_tag="JCP92_RS15330"
                     /old_locus_tag="JCP92_15330"
     CDS             1062..1595
                     /locus_tag="JCP92_RS15330"
                     /old_locus_tag="JCP92_15330"
                     /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            1607..1810
                     /locus_tag="JCP92_RS15335"
                     /old_locus_tag="JCP92_15335"
     CDS             1607..1810
                     /locus_tag="JCP92_RS15335"
                     /old_locus_tag="JCP92_15335"
                     /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            2132..2512
                     /locus_tag="JCP92_RS15340"
                     /old_locus_tag="JCP92_15340"
     CDS             2132..2512
                     /locus_tag="JCP92_RS15340"
                     /old_locus_tag="JCP92_15340"
                     /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            2494..3408
                     /locus_tag="JCP92_RS15345"
                     /old_locus_tag="JCP92_15345"
     CDS             2494..3408
                     /locus_tag="JCP92_RS15345"
                     /old_locus_tag="JCP92_15345"
                     /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            3653..4342
                     /locus_tag="JCP92_RS15350"
                     /old_locus_tag="JCP92_15350"
     CDS             3653..4342
                     /locus_tag="JCP92_RS15350"
                     /old_locus_tag="JCP92_15350"
                     /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            5225..6175
                     /locus_tag="JCP92_RS15360"
                     /old_locus_tag="JCP92_15360"
     CDS             5225..6175
                     /locus_tag="JCP92_RS15360"
                     /old_locus_tag="JCP92_15360"
                     /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"
     Typing          5227..6175
                     /name="rep_cluster_1197"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="84.953"
                     /coverage="99.0"
                     /evalue="0.0"
     Typing          2495..3405
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="94.079"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 aaaaatgagc gtggttataa ggttgtattg cgttctggag tattgcaact tgctcgcaac
       61 ttaggcaacc aaatgttgct agataggttg cacgagtacg aacaagacaa cgataaaaat
      121 gttaatatac caagcaaaaa cgtggttaca aacaagttgc tagatcagtt gcgtgaagaa
      181 aatgaatttt tacgagaaca acttgccctc agagagcaaa ataattctca tatacaaaaa
      241 ctactcgacc agcaacaaca actcacccta caagccaaca aacaaatcga aaaactgcaa
      301 gaaaaactac agttgactta tacagaagaa gctccagaga atgactcaac gactctttct
      361 gaagcaacag aaacaataga caaacaaatt gatactgaaa aaaaatggtg gcaactttgg
      421 aaataactgg agggaacatt catgacaaga aaaaatcttc tattcggttc tattttacta
      481 ggaattctag gattcagtcc gatgttattg tcagtgatca ataaagggaa taaacatggt
      541 gaattgaaat tgaatccaaa ttattacaac agtcctaacg aagaattgtt tgtaaaagaa
      601 acagataaat aataaaaaag actgctcttt cgagcagcca gttaaaaaat aatgagtgtt
      661 tattcttgaa aaagcaacgc gcttatgaag cgctaccaaa aatttatcat attttattaa
      721 aaataacaac ccagtaaaaa atgactggta aaaattcaca aagaaacgga aagaagcaac
      781 cgcagaaaat caagcttaaa aagagctttt gacctagacc aatcgaaaat cacaaagtga
      841 gcctctgtat cggttgatac aagggctact tggcatagta cacattatgt caacaagaat
      901 ttaatataac atattttcct aatgcattct aactatacca cattatcaaa aatataaatt
      961 atctttacta aataaaatat tgacaagcct ataccttttg ttttatgatt ttcacaaaga
     1021 aaacgttttc tatatatttt tctgtatcag gaggaaattc tatgaaaaaa tttactttag
     1081 gggtagcttt gttaactatt ggggcagttg ttttaccgtc aactactata gtttatgctt
     1141 cagaaaattc ccaagtggta tcattaaacg aaaacaatgc tactgaaaat gtagttattg
     1201 agtacactga agatggtatg gtcgtaacta aatatgagga tggttatagt gcggaagatt
     1261 ttgcaaattc ttcagatatc atgacaagag ctgcagttgc aagatggggc aaaaaggaat
     1321 atacaaatat tgctgtaacc actggagtag ctgctaatgc tattaatgct gccttttggg
     1381 caggagggaa agctagcact tctatgtttg gtatcccagg ttgggcaatt ggtgctttgt
     1441 taacaggtgc aagttggact aaaaaaggtg cttctccagg gaatgcagtt gcaaaagaat
     1501 gggacaaaaa tggtaatggc tggattggat tttattacca aaggggatat gatgcagctg
     1561 gaagagttgt agctactaga tattcaacgt tataagttaa ggagtgatgt ttttgatatc
     1621 taaatcatta aaatcattaa aaacatttac taaaaagaat ccgcaaatag ctactattcg
     1681 tatttttata tttgctatag ctgttgctat aattgttaat atgctaagcg gagggcaatt
     1741 atacaaatct ggtttatttt tagtgttaat cttagttgtc ttagacataa taaagtctaa
     1801 aaaaaaataa atcgatacat tttagaagaa tagggttgtt tgaatattac aaagcaacaa
     1861 tttcaccttc ggtgaaataa gcgaaacttt acaaaaagtg gctagcaaat gctagccttt
     1921 ttttgtattg tggagcgtgg attttgaggg ggattcaagg gggagcttgc gctcctttga
     1981 caagcggtta tttgcaccaa atacggaggt atttggctag caaatataga gcttgccaaa
     2041 cccttttagt gagctttact cattgtacct ttttaggtac aatggtattg cgaacgatac
     2101 gtccgtagga cgtactgaaa gggtgggact tatgagcgaa caacatcaaa atttggctag
     2161 cgatcattct aaaaaatata cctatcgatc cgagccaaaa caaatcagtt ttcgagtgag
     2221 cgaatccgaa tttgcaaagc tgaagcagtc agctgaagct ttgcaaatga gtgtgccggc
     2281 tttcgtgaaa gccaaggcac aaaacgcgcg tctggtgaca ccgaaagtgg cgccagacat
     2341 tgcccaggca atcgcgcgcg atttagccaa agctggaggg aatatcaatc aaattgccaa
     2401 gtggtgcaat acacaccaac acgacgttgc tcctgatgat gctcaacgtt tatccgaaaa
     2461 cctaaaaatc atgcaaaagg agctacaaaa gatatggcaa cagttaaagt aagtcgaacc
     2521 acttcatgta gccgagcaat caattacgca gaaccacgag caaccgtcaa aacaggaata
     2581 aactgtgaca ttgattatgc caaaagtgaa atgaaacaaa tacgcacgct ttatggaaaa
     2641 gacgatcgtg tacaagcaca cttattgatt cagtcctttc gaccaggaga aattaccgct
     2701 gaaaaagcca atcaactagg ggcagagtat gcgaaaaaaa tagcccctaa ccaccaaatc
     2761 gcgatttaca cacatacaga caaagaccat attcataatc acattgtcat taactccgtt
     2821 aatcttgaaa ctgggaaaaa atttcaagcc catgggcaag catttttaaa caaatgttat
     2881 gacctaaatg acgagatttg tcttgaacat gacttaacaa tcacggaacg aggaaagaaa
     2941 accgaaaaac gaaccatgtc tgaaattaaa ttaaaagaaa aaaatgaacc ggtttggaaa
     3001 gacgaaattc ggtttgcgat tgatcaaaca atgaaaaaca aaaaaactcg aacgtatacc
     3061 caattttgtg attcacttaa aacattcggc attcattgct tgaatcgcgg aaaaaatttt
     3121 acttacgaat tggtccacaa aaagaaaaaa gtacgatcca acaaactagg aaaggattac
     3181 gaaaaggaga cgattttaca tgagctggac agacgagaac gaacctacaa tcaacaacga
     3241 accaacgagc tacgaagagc tcgagctagc attcgcgaaa ctgcagaaga agtacgaaga
     3301 gaacaacgaa cttttacgcc tgaacaatcg gaaattagac cgactcgaag aaaccatgaa
     3361 caacacgttg aacgaggaac agaccaccaa caagaattat cgctctaaaa cgttaaaaga
     3421 catcgaaaac gaaataaaga gacaacgtgc ctttcttgcg ccttataccc aagaaaggat
     3481 acaaactacg atggattcac aagtcaaaaa actccaccaa gcgctattag accagcgaaa
     3541 ccaagaacaa aaaaaggctt taattcaacg atcgatggat attcttgccc ccttatgttg
     3601 cttagtacta acattattag ccttttggtt ggtatgggga gaataaacag acatggcatt
     3661 ctatttaccc tatctactca tttctgccag tattttagga attatttggc ttagctataa
     3721 ggcttatcaa acaagatatt cattaaaagg ctctaaaatt cgatttaagc gatttttatt
     3781 ggtcggggtt atatttgcct tatcaatcgt tttaagtggt ttattcggcg ttttagaggg
     3841 taataaacgt gtttcaagaa gcattttatt aggggatatc actcaaaagt atgaagcagc
     3901 atgtgataaa aagaaaaaag agcaagcatt agcacaaaaa atggaggaat ttaccgcttg
     3961 ttatgaggac atgaacaata tttttgtgga tcaagagaaa cgtttaacag ataaaaacat
     4021 gaaaaaactc actcgttttt atcaaaactt accagaaaaa cagcaaaaag aggtacaaga
     4081 aaaatatgag caagtaaaaa aagacgtgca atattttaaa gatacgcaga cagaagaagc
     4141 ttgttgtaac ttatttagcg atacaatccc tttttcaacc agtgaacaag aacgaaaaga
     4201 acggcaacaa tcggtcacat acgaacgtta tgaaacactg cttcagcaag caacaaacat
     4261 acaaaatcca acgaaaaaag aaacggcatt aaattatcta gaaagtgtca aggaatggtt
     4321 ggatcagcaa caacaaaatt gaatttgatt agcaatcatg ttaaactgaa cctgcaaatg
     4381 atcaaacatt agatacacga aagccccaga gaggtcggat tctctggggc tttttttcag
     4441 gttgatgtcg cctttattga ttttacttct tgtttcggtt attcaaccaa taactgaata
     4501 aagagacaca aacttctaca agaagggggc aaatgaaccg ttcaaacatt agatacacct
     4561 ccttccagtc gcaagactgt cggataggcg acaagttatt ataccttaca aaataaaatc
     4621 tgtgtggtgt ttttaagtat cccttatttt cgggttgtta gggcttgccc tgaccgcctg
     4681 taaggcgctt taagaacaag ataaggtttt ttacccaaga ctgtcttaaa acgacttaga
     4741 cgagctatca gaggcttccc ccacctccgt tactgacttg tttttagcaa aggagccttt
     4801 aggcgactgc gcagtacaat gtgagagcat agcgatcaca cttttttagc gaccgtaggg
     4861 agcaaggttt tgaattggca gttttgaaaa atgcgcgaac ctgttggtag aaaaaagaag
     4921 tggtttttag gcgggaaatt ttgtcaccct cttttataat ctctttttaa accttttttt
     4981 aaacctcttt accgtcggct gtgtcctaac tccttcaatg gatacagcgt tttataaact
     5041 acattttgtc tgcttttaaa ctacattttg tctgctttta aactacattt tgtctgcttt
     5101 taaactacat tttgtctgct tttaaactct ttttttgcac tcacgtatgt tataatatgc
     5161 attatcacag acaaaacgtt gtttataacg tctgtatcca ttgaaggagt aaggaggaat
     5221 atctttggca aatgaaatcg tgaaatacca tcatgaatta aataccattc cgttgcggaa
     5281 atttacacca gttgaaatga atctattttt ctctattgtg tctagaatgc gcgaaaaagg
     5341 cgataaaaca gtccgtctta cttttgacca actaaaagat ttaagtaatt ataaagcaac
     5401 tgctaataat cgtttcatta atgatttaga aatgacttat gataaattaa tggatttacg
     5461 ttttggtaaa agaagtgcta atgggctcga tatagataga ttcgttatgt ttagtgagtt
     5521 taaaatacgt ggaactgcta aagatccata tgtagacata caagtttacg aaaaagcttt
     5581 acctttacta aacaatttag atgagtgggt tcgctattca ctccaacaat ttaacgaatt
     5641 acaaagtagc tatgcaaaga ctatgtttcg attactaaaa caatatcgaa ctaaaggttt
     5701 tgcttatttt tctaaagagg attttcatga actattagat attccaaaaa gttactggaa
     5761 caaccaagca aacgttgata atcgtgttat aaagcctata cgacaggaat taaccgcaat
     5821 cttcaaagga ttatcaatca aaaagaaata cggaaaaggg cgaggaaaac ctgtcgttgg
     5881 ctatcaattt acgtttaaac cagaaatcaa aaaagcagat gattttaata aacatgcacc
     5941 aaccaaagaa gaacaaaata aagcattggc tttagctgat aaacaaaaag aatacgaaga
     6001 acctgctaca acaattaacg aaaaaatcaa acagaagaaa cgagaacttg aactcctcca
     6061 acaaatcaaa caactagaaa aagagaaaga agctcttgaa aaacaaacag agtccgcact
     6121 ttcgaaaaaa gagaaaaaaa gtttattatc tgatttagat aatttattcc agtagcaacc
     6181 taggaggcaa ccagtatgca accacaagaa acctttacaa taaaggaatt gtcagaactt
     6241 tttaagatga gtaggcaagc aatatcgaaa catatccaaa aattagattc ttccatgata
     6301 gct
//
