LOCUS       NZ_CP124897             5121 bp    DNA     circular CON 15-MAY-2024
DEFINITION  Enterococcus faecalis strain EfsC116 plasmid p3_EfsC116_rep6,
            complete sequence.
ACCESSION   NZ_CP124897
VERSION     NZ_CP124897.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN33741209
            Assembly: GCF_030020475.1
KEYWORDS    RefSeq.
SOURCE      Enterococcus faecalis
  ORGANISM  Enterococcus faecalis
            Bacteria; Bacillota; Bacilli; Lactobacillales; Enterococcaceae;
            Enterococcus.
REFERENCE   1  (bases 1 to 5121)
  AUTHORS   Sharon,B.M., Arute,A.P., Nguyen,A., Tiwari,S., Bonthu,S.S.R.,
            Hulyalkar,N.V., Neugent,M.L., Dillon,N.A., Zimmern,P.E., Palmer,K.L.
            and De Nisco,N.J.
  TITLE     Functional and genetic adaptation of urinary Enterococcus faecalis
            identified by comparative genomics
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 5121)
  AUTHORS   Sharon,B.M.
  TITLE     Direct Submission
  JOURNAL   Submitted (14-MAR-2023) Biological Sciences, University of Texas at
            Dallas, 800 W Campbell Road, Richardson, TX 75080, USA
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: Unicycler v. v.0.4.8
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 451x, 241x
            Sequencing Technology             :: Illumina NextSeq, ONT MinION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_030020475.1-RS_2024_05_15
            Annotation Date                   :: 05/15/2024 05:01:09
            Annotation Pipeline :: NCBI Prokaryotic Genome Annotation Pipeline
            (PGAP)
            Annotation Method :: Best-placed reference protein set; GeneMarkS-2+
            Annotation Software revision      :: 6.7
            Features Annotated                :: Gene; CDS; rRNA; tRNA; ncRNA
            Genes (total)                     :: 3,030
            CDSs (total)                      :: 2,951
            Genes (coding)                    :: 2,903
            CDSs (with protein)               :: 2,903
            Genes (RNA)                       :: 79
            rRNAs                             :: 4, 4, 4 (5S, 16S, 23S)
            complete rRNAs                    :: 4, 4, 4 (5S, 16S, 23S)
            tRNAs                             :: 63
            ncRNAs                            :: 4
            Pseudo Genes (total)              :: 48
            CDSs (without protein)            :: 48
            Pseudo Genes (ambiguous residues) :: 0 of 48
            Pseudo Genes (frameshifted)       :: 23 of 48
            Pseudo Genes (incomplete)         :: 23 of 48
            Pseudo Genes (internal stop)      :: 12 of 48
            Pseudo Genes (multiple problems)  :: 10 of 48
            CRISPR Arrays                     :: 1
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP124897.1.
            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..5121
                     /organism="Enterococcus faecalis"
                     /mol_type="genomic DNA"
                     /strain="EfsC116"
                     /isolation_source="urine"
                     /host="Homo sapiens"
                     /db_xref="taxon:1351"
                     /plasmid="p3_EfsC116_rep6"
                     /geo_loc_name="USA: Dallas, Texas"
                     /lat_lon="32.77 N 96.79 W"
                     /collection_date="2019-04"
                     /collected_by="UT Southwestern Medical Center/ UT Dallas"
     gene            1..723
                     /locus_tag="QLQ63_RS15090"
                     /old_locus_tag="QLQ63_15090"
     CDS             1..723
                     /locus_tag="QLQ63_RS15090"
                     /old_locus_tag="QLQ63_15090"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_002360724.1"
                     /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_002360724.1"
                     /translation="MSDKSELAVKYQNELNLVPLKNFNAKQMDLFFALCARMKDKGVEN
                     IRFSFEELKELSDYKMTATKAFVADLEKLYKDMLNLSYRTENDDEIEYFVLFNGFKIDK
                     KQKFVEVRVNQDLDYIINGLTTEFSRFELSAFTSIRSTYAKTLFRLLMQYRSTGYYVVS
                     IEDFRELLDIPEYYQMGNIDQKVLKPAMKELHNYFENLEVTKIKAKKGNKIAKLEFTFT
                     GLKTNKPSVTMHDWVNGE"
                     /name="replication initiation protein"
     gene            850..1146
                     /locus_tag="QLQ63_RS15095"
                     /old_locus_tag="QLQ63_15095"
     CDS             850..1146
                     /locus_tag="QLQ63_RS15095"
                     /old_locus_tag="QLQ63_15095"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_002404941.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_002360723.1"
                     /translation="MGLMTGYNMTKEEYEVTQAVLERLDKFESELEALLLDLEPLDLSR
                     LDTVVRDETLRMFNYLSRSYILLIDTVAYKVTLEEDISCGIVKIDGQSLDEEE"
                     /name="hypothetical protein"
     gene            1924..3603
                     /gene="mobV"
                     /locus_tag="QLQ63_RS15100"
                     /old_locus_tag="QLQ63_15100"
     CDS             1924..3603
                     /gene="mobV"
                     /locus_tag="QLQ63_RS15100"
                     /old_locus_tag="QLQ63_15100"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_002401964.1"
                     /GO_function="GO:0003677 - DNA binding [Evidence IEA]"
                     /GO_process="GO:0006310 - DNA recombination [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MobV family relaxase"
                     /protein_id="WP_282853606.1"
                     /translation="MSKIVARMEKMKDGNLSGIQRHNQRETNNHSNPDIDIEKSHLNYD
                     LVNPGSINYREKIKQIIESQRISKRAVRKDAVLVNEWIITSDTAFFQENTDTQAFFTDV
                     VAYFSDRCGRQNVAYATVHLDETTPHMHLGIVPMYEGRLSSKQVFSRQNLLEIQEELPT
                     YLQERGYAIERGLRGSPQKHLSVKEYKDVQKELQVSKQELANQEQILAEKERELHSYEQ
                     AIFRIDRLLEEKNEEVKGKVQAMNQLETKRNEIINSLQTTVLPDLANVKEKKFSLNGLK
                     YVLSASDFSAIKSITKDFETLRTQNKHLKIENNNLAQKNKELTQVNHEQELQITELAYE
                     LTLKKEQLTAFEEKQLNYDQSEQIKQELDTTTQTVSVLETENKRLKDKITDLTYDFSEL
                     NEKYQEIKLKFDGLTTYLHERLGHAKETILFTIQQGVKHLQNAPKLKKSLERYSKDRTY
                     LIDEKGTLFLPPDTGSKGVTMSLNPHFYPLKAPFYNRETGCYEFVGEYMANGRSRTNTL
                     QLSEEQVLEKKAFTFEQSTDKKAWQQSKKYSRDMSKGRGLSR"
                     /name="mobV"
     gene            3692..3892
                     /locus_tag="QLQ63_RS15105"
                     /old_locus_tag="QLQ63_15105"
     CDS             3692..3892
                     /locus_tag="QLQ63_RS15105"
                     /old_locus_tag="QLQ63_15105"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_016632908.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_002364281.1"
                     /translation="MKKLLVLILGVSFISVALSSTTEASAREWDSIECQPGFYWKKGGW
                     TAGGYHKAGGFCIPMHTRWTK"
                     /name="hypothetical protein"
     gene            complement(4411..4497)
                     /locus_tag="QLQ63_RS15110"
                     /old_locus_tag="QLQ63_15110"
     CDS             complement(4411..4497)
                     /locus_tag="QLQ63_RS15110"
                     /old_locus_tag="QLQ63_15110"
                     /inference="COORDINATES: protein motif:HMM:NF033608.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="type I toxin-antitoxin system Fst family toxin"
                     /protein_id="WP_107196852.1"
                     /translation="MIESLISLIIAPLFVGLVLLLVDRWLDD"
                     /name="type I toxin-antitoxin system Fst family toxin"
     Typing          complement(1379..1638)
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="80.0"
                     /coverage="81.0"
                     /evalue="1.95e-45"
     Typing          2..723
                     /name="rep_cluster_2301"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          1850..3600
                     /name="MOBV"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="99.829"
                     /coverage="99.0"
                     /evalue="0.0"
ORIGIN
        1 atgagtgata aatcggaatt agctgttaaa tatcaaaatg agttaaatct tgtgccactt
       61 aaaaacttta atgcaaaaca aatggatctg ttctttgcgt tatgcgcacg aatgaaagat
      121 aaaggagtag agaatattcg tttctccttc gaggaattaa aggaattgag tgactacaaa
      181 atgactgcta caaaagcctt tgtagcagac ttagaaaagt tgtataaaga tatgctgaac
      241 ctttcttatc gtacagaaaa cgatgacgaa atagagtatt ttgttttatt caatggattt
      301 aaaatcgaca aaaaacaaaa gtttgttgaa gttcgagtta atcaagattt agactatata
      361 ataaatggtt taacaacaga gtttagtagg tttgagctgt ccgcttttac ttcaatacgc
      421 tcaacatatg ctaaaacatt gtttcgtttg ttaatgcaat atcgttcaac agggtattat
      481 gtagtcagta ttgaagactt cagagaattg ttagacatac ccgaatatta tcaaatgggt
      541 aacattgacc aaaaggtttt aaaaccagca atgaaagaac tccataacta ttttgagaat
      601 ttagaagtaa caaaaatcaa agccaaaaaa ggcaataaga ttgccaaact agaatttacg
      661 tttactggtc tgaaaaccaa caaaccaagc gtaaccatgc acgattgggt aaacggagaa
      721 taaaaaaaga acttgccccc tcacattaag caagttagca agttcctcac gcaatcttcc
      781 ggactgctag attattttag catatttgcg tgaggacttc taaaataaat tattttggag
      841 gtcctactta tgggattaat gacaggatac aacatgacaa aagaggagta cgaagtcaca
      901 caggctgtac tggagcgact agataagttt gagagtgaac tagaagcgct attgcttgat
      961 ttggagccac ttgacttatc acgattagat actgtagttc gagacgaaac gctaagaatg
     1021 tttaattatc taagtcggtc atacattcta cttattgata cggtagccta caaagttacg
     1081 ctagaagaag atatttcctg tgggattgtg aagattgacg gtcaatctct agacgaagaa
     1141 gaataaaaac tacccttgct tgttataaaa aaatgttgac tatttgggat aacactcgaa
     1201 aaatatcaag attagcctac ttccattttg gggtaggctt tctttttgca agcggagcaa
     1261 catggtacca tgttgcgata ttttgaacga ctcctaccaa aaatactggt aggagtcgtt
     1321 caaatttttg gggttccccc aatcccactg ctgttatttt ttgcttttac tgttgaaatt
     1381 cgcttaattt cttcctgtgt ttcggaagag cataagggga actggggggc acacaaggta
     1441 ccccgccttg cagtgcaagg ctttcccgtg gggtacactt tcgttcttcg ctagcacttt
     1501 actagcaggt actttcaggt aaactagcac atttttagca ctcaatagca ggtttctagc
     1561 acccaaacta gcagattcct agcagtgact agcaggtttt tagcaccaaa ttagcacatt
     1621 actagcaccg gctagcagaa agctagcacg ttcactaatt tcaggcagtc gttatttaaa
     1681 cggttttctg acggagggaa atttggagtt tctgccttag cagaaatgga aagtttgacc
     1741 gtaggcaatc ggctaagtgc gagattggga agcctaaagg ctgacctttc gagtactagc
     1801 cgacagccct cggcagagcg cacctttacg aagtaaagta tagtgcgtta tactttactt
     1861 ggaagtactg ccgaaatcca aagacaccga acgacacaag aaaaaaaagg gggaggagcg
     1921 ctcatgtcaa aaattgttgc acgtatggaa aaaatgaaag acggaaattt aagtggtatc
     1981 caacgacata atcaacgaga aaccaataat cattccaatc ctgatattga tattgagaaa
     2041 tctcacttga attatgactt agtcaatcct ggttcaatca attatcggga gaaaatcaaa
     2101 caaatcattg agagccaacg aatcagtaaa cgagcggtta gaaaagacgc agtccttgtg
     2161 aacgaatgga taatcactag tgataccgcc ttttttcaag agaatacaga cacacaagca
     2221 ttttttaccg atgttgtcgc atatttctct gatcgctgcg gtcgacaaaa tgtcgcctat
     2281 gccacggtac atttagacga aaccacgccc catatgcact taggaattgt gcctatgtac
     2341 gaagggcgat tgagcagtaa acaggtgttt agtcggcaaa atttgttaga gattcaagaa
     2401 gaattgccaa cctatttgca agaacgaggc tatgctattg agcgtggact ccgtgggagt
     2461 ccgcaaaagc atttatctgt caaagaatac aaagacgttc aaaaggagct acaagtttct
     2521 aagcaggaac tcgctaatca ggaacaaatt ctggcagaaa aagagagaga actccattct
     2581 tatgaacagg caatcttccg tattgaccgc cttcttgaag agaagaacga agaagtaaag
     2641 ggcaaagtcc aagcaatgaa ccaactggaa acgaagcgaa acgaaatcat taactctcta
     2701 caaacaaccg ttttacctga tttagcaaat gtcaaagaaa agaaatttag tttaaacggt
     2761 ttaaaatacg ttttaagcgc ttctgacttt tcggcgataa aaagtattac gaaagatttc
     2821 gagacgctta gaacgcaaaa taagcacctt aaaatcgaaa acaataactt ggcacagaaa
     2881 aataaagaat tgacacaagt aaatcatgaa caagaattac aaataacgga attagcctat
     2941 gaattaaccc tgaaaaaaga acaattaaca gcgtttgaag aaaaacaact aaactatgac
     3001 cagagcgaac aaatcaaaca agaacttgat acaacaacac aaacagtttc tgtgttagaa
     3061 acagagaata agcggttaaa agataaaatt actgacttaa cctacgactt ttctgaacta
     3121 aatgaaaaat atcaagaaat aaaattaaag tttgacgggt taactactta ccttcacgaa
     3181 agactaggtc atgctaaaga aaccatttta tttacgattc agcaaggagt gaagcacctt
     3241 cagaacgcgc ctaaattaaa aaaatcccta gagcgatatt ccaaggatag aacttacctc
     3301 attgacgaaa aagggacatt gtttttacca ccagatacgg ggtcaaaagg ggtaacaatg
     3361 tccttaaacc cacatttcta ccccctaaaa gccccgtttt acaacagaga aacagggtgt
     3421 tatgagtttg tcggcgaata tatggctaat ggacgttctc gaacgaatac tttacaactg
     3481 tctgaagaac aagtgctaga gaagaaagct tttacgtttg aacagtcgac agataaaaag
     3541 gcttggcaac agagtaaaaa atattcaaga gatatgtcaa aaggacgagg tttatctcgt
     3601 taaaaataat ttaattgata aattattgac acataaaaac agttaaatta aaatatatta
     3661 ataaaaatta aaaaaaagtg aggtaagcat tatgaaaaag ttgttagttc taattttagg
     3721 ggtgtctttt atctctgttg ctttaagttc aactacagaa gcaagtgcta gagagtggga
     3781 ttctatagag tgtcagccag gattttattg gaaaaaaggc gggtggactg caggaggata
     3841 tcataaagcc ggtggatttt gtatcccaat gcatacaaga tggacaaaat agttgctaaa
     3901 tttgaggtta tttcatgaaa aaatatctaa taaaaaatat attttatatt actattcctt
     3961 tagttttaag ctatataact tcttttttag ttaatattga tttgcccata ttgataatta
     4021 ttttttacgg aattttatta ttttttttaa ttccttcaga agtatatttg ggaagtacaa
     4081 tggattacaa cgcgaaagta gtgaatccca cttacagacc agaaaataaa agctttgaag
     4141 atagtccaaa aagtaaaata ttgtctatcc tcatagtatt actatgttta atactaacta
     4201 tttcgatatg gtatttctct aattgacgtt ttgcgtaatc taatctgatg tttgaaaata
     4261 cagaaaaaaa atgttattgt gtaagtgcga agcgaaatta agcaaaatca tgtttacacc
     4321 aaaaagccct cctattctca gtaggagggc ttttttacac tgttgcgatt tcagcgttgg
     4381 agctagaaaa gcaactgcat agattatctg ctaatcgtct agccaacgat caactagcaa
     4441 aagtactaaa cccacaaaaa gtggggcgat aatcaacgaa attaagcttt caatcatgtt
     4501 tacaccccct ttcggggcag ttgccaaaac aagtatatca caagaagaat ttcttgtggg
     4561 ggttgttagg gcttgccctg accgcctgca aggcgcaatc ctaaccaaga taccctaaaa
     4621 caactaaaca tgtcttaaag atcttcagac aagcaaatag agcctaacca aatgatttac
     4681 cttgtcaacg gtattgattt tgattttagc gagtgaacga agtgaacgct gcaagcaaaa
     4741 tgtgagcggg attttcgctc actccttttt tgatttttta gtgccagttt tgtaaatatc
     4801 gcggacctgt ttgtagaaaa aagaggttaa ttttgggcgg gaaatttccg cgcgcgcacg
     4861 cgtttctttt atatatattt tatatatatt tttaaaacct ttttaggcgg gctgtgtgcc
     4921 acgtggctct aaggaagagc agatggtacc aacaactttt tatctgacta ccaacaactt
     4981 tttatctgac taccaacaac tttttatctg actaccaaca actttttatc tgttttattt
     5041 tcataatatt aaaacaaaca accaactgtt gacaaagttg gttgtttgtt ttaatattcg
     5101 aattgtgagg gggcgaaagg a
//
