LOCUS       NZ_CP066419             6303 bp    DNA     circular CON 19-FEB-2024
DEFINITION  Enterococcus faecium strain Dallas 53_1 plasmid p53_1_6.3kb,
            complete sequence.
ACCESSION   NZ_CP066419
VERSION     NZ_CP066419.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN17038078
            Assembly: GCF_016406365.1
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  JOURNAL   Unpublished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                   :: 256.0x
            Sequencing Technology :: Illumina NextSeq; Oxford Nanopore MinION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 02/19/2024 03:59:44
            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)                     :: 3,131
            CDSs (total)                      :: 3,040
            Genes (coding)                    :: 2,918
            CDSs (with protein)               :: 2,918
            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)              :: 122
            CDSs (without protein)            :: 122
            Pseudo Genes (ambiguous residues) :: 0 of 122
            Pseudo Genes (frameshifted)       :: 44 of 122
            Pseudo Genes (incomplete)         :: 72 of 122
            Pseudo Genes (internal stop)      :: 30 of 122
            Pseudo Genes (multiple problems)  :: 20 of 122
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP066419.1.
            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_1"
                     /isolation_source="rectal swab"
                     /host="Homo sapiens"
                     /db_xref="taxon:1352"
                     /plasmid="p53_1_6.3kb"
                     /geo_loc_name="USA: Dallas"
                     /collection_date="2015"
     gene            308..841
                     /locus_tag="JCP73_RS15505"
                     /old_locus_tag="JCP73_15495"
     CDS             308..841
                     /locus_tag="JCP73_RS15505"
                     /old_locus_tag="JCP73_15495"
                     /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            853..1056
                     /locus_tag="JCP73_RS15730"
                     /old_locus_tag="JCP73_15500"
     CDS             853..1056
                     /locus_tag="JCP73_RS15730"
                     /old_locus_tag="JCP73_15500"
                     /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            1378..1758
                     /locus_tag="JCP73_RS15515"
                     /old_locus_tag="JCP73_15505"
     CDS             1378..1758
                     /locus_tag="JCP73_RS15515"
                     /old_locus_tag="JCP73_15505"
                     /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            1740..2654
                     /locus_tag="JCP73_RS15520"
                     /old_locus_tag="JCP73_15510"
     CDS             1740..2654
                     /locus_tag="JCP73_RS15520"
                     /old_locus_tag="JCP73_15510"
                     /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            2899..3588
                     /locus_tag="JCP73_RS15525"
                     /old_locus_tag="JCP73_15515"
     CDS             2899..3588
                     /locus_tag="JCP73_RS15525"
                     /old_locus_tag="JCP73_15515"
                     /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            4471..5421
                     /locus_tag="JCP73_RS15535"
                     /old_locus_tag="JCP73_15525"
     CDS             4471..5421
                     /locus_tag="JCP73_RS15535"
                     /old_locus_tag="JCP73_15525"
                     /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            5442..5975
                     /locus_tag="JCP73_RS15540"
                     /old_locus_tag="JCP73_15530"
     CDS             5442..5975
                     /locus_tag="JCP73_RS15540"
                     /old_locus_tag="JCP73_15530"
                     /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            5991..6161
                     /locus_tag="JCP73_RS15545"
                     /old_locus_tag="JCP73_15535"
     CDS             5991..6161
                     /locus_tag="JCP73_RS15545"
                     /old_locus_tag="JCP73_15535"
                     /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          4473..5421
                     /name="rep_cluster_1197"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="84.953"
                     /coverage="99.0"
                     /evalue="0.0"
     Typing          1741..2651
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="94.079"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 ttcacaaaga aacggaaaga agcaaccgca gaaaatcaag cttaaaaaga gcttttgacc
       61 tagaccaatc gaaaatcaca aagtgagcct ctgtatcggt tgatacaagg gctacttggc
      121 atagtgtaca ttatgtcaac aagaatttaa tataacatat tttcctaatg cattctaact
      181 ataccacatt atcaaaaata taaattatct ttactaaata aaatattgac aagcctatac
      241 cttttgtttt atgattttca caaagaaaac gttttctata tatttttctg tatcaggagg
      301 aaattctatg aaaaaattta ctttaggggt agctttgtta actattgggg cagttgtttt
      361 accgtcaact actatagttt atgcttcaga aaattcccaa gtggtatcat taaacgaaaa
      421 caatgctact gaaaatgtag ttattgagta cactgaagat ggtatggtcg taactaaata
      481 tgaggatggt tatagtgcgg aagattttgc aaattcttca gatatcatga caagagctgc
      541 agttgcaaga tggggcaaaa aggaatatac aaatattgct gtaaccactg gagtagctgc
      601 taatgctatt aatgctgcct tttgggcagg agggaaagct agcacttcta tgtttggtat
      661 cccaggttgg gcaattggtg ctttgttaac aggtgcaagt tggactaaaa aaggtgcttc
      721 tccagggaat gcagttgcaa aagaatggga caaaaatggt aatggctgga ttggatttta
      781 ttaccaaagg ggatatgatg cagctggaag agttgtagct actagatatt caacgttata
      841 agttaaggag tgatgttttt gatatctaaa tcattaaaat cattaaaaac atttactaaa
      901 aagaatccgc aaatagctac tattcgtatt tttatatttg ctatagctgt tgctataatt
      961 gttaatatgc taagcggagg gcaattatac aaatctggtt tatttttagt gttaatctta
     1021 gttgtcttag acataataaa gtctaaaaaa aaataaatcg atacatttta gaagaatagg
     1081 gttgtttgaa tattacaaag caacaatttc accttcggtg aaataagcga aactttacaa
     1141 aaagtggcta gcaaatgcta gccttttttt gtattgtgga gcgtggattt tgagggggat
     1201 tcaaggggga gcttgcgctc ctttgacaag cggttatttg caccaaatac ggaggtattt
     1261 ggctagcaaa tatagagctt gccaaaccct tttagtgagc tttactcatt gtaccttttt
     1321 aggtacaatg gtattgcgaa cgatacgtcc gtaggacgta ctgaaagggt gggacttatg
     1381 agcgaacaac atcaaaattt ggctagcgat cattctaaaa aatataccta tcgatccgag
     1441 ccaaaacaaa tcagttttcg agtgagcgaa tccgaatttg caaagctgaa gcagtcagct
     1501 gaagctttgc aaatgagtgt gccggctttc gtgaaagcca aggcacaaaa cgcgcgtctg
     1561 gtgacaccga aagtggcgcc agacattgcc caggcaatcg cgcgcgattt agccaaagct
     1621 ggagggaata tcaatcaaat tgccaagtgg tgcaatacac accaacacga cgttgctcct
     1681 gatgatgctc aacgtttatc cgaaaaccta aaaatcatgc aaaaggagct acaaaagata
     1741 tggcaacagt taaagtaagt cgaaccactt catgtagccg agcaatcaat tacgcagaac
     1801 cacgagcaac cgtcaaaaca ggaataaact gtgacattga ttatgccaaa agtgaaatga
     1861 aacaaatacg cacgctttat ggaaaagacg atcgtgtaca agcacactta ttgattcagt
     1921 cctttcgacc aggagaaatt accgctgaaa aagccaatca actaggggca gagtatgcga
     1981 aaaaaatagc ccctaaccac caaatcgcga tttacacaca tacagacaaa gaccatattc
     2041 ataatcacat tgtcattaac tccgttaatc ttgaaactgg gaaaaaattt caagcccatg
     2101 ggcaagcatt tttaaacaaa tgttatgacc taaatgacga gatttgtctt gaacatgact
     2161 taacaatcac ggaacgagga aagaaaaccg aaaaacgaac catgtctgaa attaaattaa
     2221 aagaaaaaaa tgaaccggtt tggaaagacg aaattcggtt tgcgattgat caaacaatga
     2281 aaaacaaaaa aactcgaacg tatacccaat tttgtgattc acttaaaaca ttcggcattc
     2341 attgcttgaa tcgcggaaaa aattttactt acgaattggt ccacaaaaag aaaaaagtac
     2401 gatccaacaa actaggaaag gattacgaaa aggagacgat tttacatgag ctggacagac
     2461 gagaacgaac ctacaatcaa caacgaacca acgagctacg aagagctcga gctagcattc
     2521 gcgaaactgc agaagaagta cgaagagaac aacgaacttt tacgcctgaa caatcggaaa
     2581 ttagaccgac tcgaagaaac catgaacaac acgttgaacg aggaacagac caccaacaag
     2641 aattatcgct ctaaaacgtt aaaagacatc gaaaacgaaa taaagagaca acgtgccttt
     2701 cttgcgcctt atacccaaga aaggatacaa actacgatgg attcacaagt caaaaaactc
     2761 caccaagcgc tattagacca gcgaaaccaa gaacaaaaaa aggctttaat tcaacgatcg
     2821 atggatattc ttgccccctt atgttgctta gtactaacat tattagcctt ttggttggta
     2881 tggggagaat aaacagacat ggcattctat ttaccctatc tactcatttc tgccagtatt
     2941 ttaggaatta tttggcttag ctataaggct tatcaaacaa gatattcatt aaaaggctct
     3001 aaaattcgat ttaagcgatt tttattggtc ggggttatat ttgccttatc aatcgtttta
     3061 agtggtttat tcggcgtttt agagggtaat aaacgtgttt caagaagcat tttattaggg
     3121 gatatcactc aaaagtatga agcagcatgt gataaaaaga aaaaagagca agcattagca
     3181 caaaaaatgg aggaatttac cgcttgttat gaggacatga acaatatttt tgtggatcaa
     3241 gagaaacgtt taacagataa aaacatgaaa aaactcactc gtttttatca aaacttacca
     3301 gaaaaacagc aaaaagaggt acaagaaaaa tatgagcaag taaaaaaaga cgtgcaatat
     3361 tttaaagata cgcagacaga agaagcttgt tgtaacttat ttagcgatac aatccctttt
     3421 tcaaccagtg aacaagaacg aaaagaacgg caacaatcgg tcacatacga acgttatgaa
     3481 acactgcttc agcaagcaac aaacatacaa aatccaacga aaaaagaaac ggcattaaat
     3541 tatctagaaa gtgtcaagga atggttggat cagcaacaac aaaattgaat ttgattagca
     3601 atcatgttaa actgaacctg caaatgatca aacattagat acacgaaagc cccagagagg
     3661 tcggattctc tggggctttt tttcaggttg atgtcgcctt tattgatttt acttcttgtt
     3721 tcggttattc aaccaataac tgaataaaga gacacaaact tctacaagaa gggggcaaat
     3781 gaaccgttca aacattagat acacctcctt ccagtcgcaa gactgtcgga taggcgacaa
     3841 gttattatac cttacaaaat aaaatctgtg tggtgttttt aagtatccct tattttcggg
     3901 ttgttagggc ttgccctgac cgcctgtaag gcgctttaag aacaagataa ggttttttac
     3961 ccaagactgt cttaaaacga cttagacgag ctatcagagg cttcccccac ctccgttact
     4021 gacttgtttt tagcaaagga gcctttaggc gactgcgcag tacaatgtga gagcatagcg
     4081 atcacacttt tttagcgacc gtagggagca aggttttgaa ttggcagttt tgaaaaatgc
     4141 gcgaacctgt tggtagaaaa aagaagtggt ttttaggcgg gaaattttgt caccctcttt
     4201 tataatctct ttttaaacct ttttttaaac ctctttaccg tcggctgtgt ccttactcct
     4261 tcaatggata cagcgtttta taaactacat tttgtctgct tttaaactac attttgtctg
     4321 cttttaaact acattttgtc tgcttttaaa ctacattttg tctgctttta aactcttttt
     4381 ttgcactcac gtatgttata atatgcatta tcacagacaa aacgttgttt ataacgtctg
     4441 tatccattga aggagtaagg aggaatatct ttggcaaatg aaatcgtgaa ataccatcat
     4501 gaattaaata ccattccgtt gcggaaattt acaccagttg aaatgaatct atttttctct
     4561 attgtgtcta gaatgcgcga aaaaggcgat aaaacagtcc gtcttacttt tgaccaacta
     4621 aaagatttaa gtaattataa agcaactgct aataatcgtt tcattaatga tttagaaatg
     4681 acttatgata aattaatgga tttacgtttt ggtaaaagaa gtgctaatgg gctcgatata
     4741 gatagattcg ttatgtttag tgagtttaaa atacgtggaa ctgctaaaga tccatatgta
     4801 gacatacaag tttacgaaaa agctttacct ttactaaaca atttagatga gtgggttcgc
     4861 tattcactcc aacaatttaa cgaattacaa agtagctatg caaagactat gtttcgatta
     4921 ctaaaacaat atcgaactaa aggttttgct tatttttcta aagaggattt tcatgaacta
     4981 ttagatattc caaaaagtta ctggaacaac caagcaaacg ttgataatcg tgttataaag
     5041 cctatacgac aggaattaac cgcaatcttc aaaggattat caatcaaaaa gaaatacgga
     5101 aaagggcgag gaaaacctgt cgttggctat caatttacgt ttaaaccaga aatcaaaaaa
     5161 gcagatgatt ttaataaaca tgcaccaacc aaagaagaac aaaataaagc attggcttta
     5221 gctgataaac aaaaagaata cgaagaacct gctacaacaa ttaacgaaaa aatcaaacag
     5281 aagaaacgag aacttgaact cctccaacaa atcaaacaac tagaaaaaga gaaagaagct
     5341 cttgaaaaac aaacagagtc cgcactttcg aaaaaagaga aaaaaagttt attatctgat
     5401 ttagataatt tattccagta gcaacctagg aggcaaccag tatgcaacca caagaaacct
     5461 ttacaataaa ggaattgtca gaacttttta agatgagtag gcaagcaata tcgaaacata
     5521 tccaaaaatt agattcttcc atgatagcta aaaatgagcg tggttataag gttgtattgc
     5581 gttctggagt attgcaactt gctcgcaact taggcaacca aatgttgcta gataggttgc
     5641 acgagtacga acaagacaac gataaaaatg ttaatatacc aagcaaaaac gtggttacaa
     5701 acaagttgct agatcagttg cgtgaagaaa atgaattttt acgagaacaa cttgccctca
     5761 gagagcaaaa taattctcat atacaaaaac tactcgacca gcaacaacaa ctcaccctac
     5821 aagccaacaa acaaatcgaa aaactgcaag aaaaactaca gttgacttat acagaagaag
     5881 ctccagagaa tgactcaacg actctttctg aagcaacaga aacaatagac aaacaaattg
     5941 atactgaaaa aaaatggtgg caactttgga aataactgga gggaacattc atgacaagaa
     6001 aaaatcttct attcggttct attttactag gaattctagg attcagtccg atgttattgt
     6061 cagtgatcaa taaagggaat aaacatggtg aattgaaatt gaatccaaat tattacaaca
     6121 gtcctaacga agaattgttt gtaaaagaaa cagataaata ataaaaaaga ctgctctttc
     6181 gagcagccag ttaaaaaata atgagtgttt attcttgaaa aagcaacgcg cttatgaagc
     6241 gctaccaaaa atttatcata ttttattaaa aataacaacc cagtaaaaaa tgactggtaa
     6301 aaa
//
