LOCUS       NZ_CP068138             2473 bp    DNA     circular CON 06-FEB-2024
DEFINITION  Staphylococcus epidermidis strain FDAARGOS_1083 plasmid unnamed2,
            complete sequence.
ACCESSION   NZ_CP068138
VERSION     NZ_CP068138.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN16357252
            Assembly: GCF_016727385.1
KEYWORDS    RefSeq.
SOURCE      Staphylococcus epidermidis
  ORGANISM  Staphylococcus epidermidis
            Bacteria; Bacillota; Bacilli; Bacillales; Staphylococcaceae;
            Staphylococcus.
REFERENCE   1  (bases 1 to 2473)
  AUTHORS   Blissenbach,B., Krut,O., Tallon,L., Sadzewicz,L., Zhao,X.,
            Boylan,J., Ott,S., Bowen,H., Vavikolanu,K., Mehta,A.,
            Aluvathingal,J., Nadendla,S., Yan,Y. and Sichtig,H.
  TITLE     FDA dAtabase for Regulatory Grade micrObial Sequences (FDA-ARGOS):
            Supporting development and validation of Infectious Disease Dx tests
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 2473)
  AUTHORS   Blissenbach,B., Krut,O., Tallon,L., Sadzewicz,L., Zhao,X.,
            Boylan,J., Ott,S., Bowen,H., Vavikolanu,K., Mehta,A.,
            Aluvathingal,J., Nadendla,S., Yan,Y. and Sichtig,H.
  TITLE     Direct Submission
  JOURNAL   Submitted (11-JAN-2021) Institute for Genome Sciences, University of
            Maryland School of Medicine, BioPark II, 801 W. Baltimore St., Suite
            619, Baltimore, MD 21201, USA
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method :: SMRT v. 8.0.0, HGAP v. 4_microbial
            Genome Coverage                   :: 2447.73x
            Sequencing Technology             :: Pacbio; Illumina
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 02/06/2024 04:36:42
            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)                     :: 2,369
            CDSs (total)                      :: 2,285
            Genes (coding)                    :: 2,222
            CDSs (with protein)               :: 2,222
            Genes (RNA)                       :: 84
            rRNAs                             :: 7, 6, 6 (5S, 16S, 23S)
            complete rRNAs                    :: 7, 6, 6 (5S, 16S, 23S)
            tRNAs                             :: 61
            ncRNAs                            :: 4
            Pseudo Genes (total)              :: 63
            CDSs (without protein)            :: 63
            Pseudo Genes (ambiguous residues) :: 0 of 63
            Pseudo Genes (frameshifted)       :: 39 of 63
            Pseudo Genes (incomplete)         :: 33 of 63
            Pseudo Genes (internal stop)      :: 25 of 63
            Pseudo Genes (multiple problems)  :: 27 of 63
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP068138.1.
            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..2473
                     /organism="Staphylococcus epidermidis"
                     /mol_type="genomic DNA"
                     /strain="FDAARGOS_1083"
                     /culture_collection="PEI:PEI-B-P-06"
                     /db_xref="taxon:1282"
                     /plasmid="unnamed2"
                     /geo_loc_name="Germany: Langen"
                     /collected_by="Paul Ehrlich Institut"
     gene            546..605
                     /gene="ermCL"
                     /locus_tag="I6I40_RS11745"
                     /old_locus_tag="I6I40_11745"
     CDS             546..605
                     /gene="ermCL"
                     /locus_tag="I6I40_RS11745"
                     /old_locus_tag="I6I40_11745"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_002497446.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="23S rRNA methylase leader peptide ErmCL"
                     /protein_id="WP_002497446.1"
                     /translation="MGIFSIFVISTVHYQPNKK"
                     /name="ermCL"
     gene            666..1400
                     /gene="erm(C)"
                     /locus_tag="I6I40_RS11750"
                     /old_locus_tag="I6I40_11750"
     ARG             667..1397
                     /name="erm(C)"
                     /gene="erm(C)"
                     /gene_name="23S rRNA (adenine(2058)-N(6))-methyltransferase
                     Erm(C)"
                     /tool="amrfinderplus"
                     /drug_class="LINCOSAMIDE/MACROLIDE/STREPTOGRAMIN"
                     /identity="100.0"
                     /coverage="100.0"
     gene            1848..2324
                     /locus_tag="I6I40_RS11755"
                     /old_locus_tag="I6I40_11755"
     CDS             1848..2324
                     /locus_tag="I6I40_RS11755"
                     /old_locus_tag="I6I40_11755"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000664727.1"
                     /GO_process="GO:0006260 - DNA replication [Evidence IEA];
                     GO:0006276 - plasmid maintenance [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="replication/maintenance protein RepL"
                     /protein_id="WP_000664727.1"
                     /translation="MKERYGTVYKGSQRLIDEESGEVIEVDKLYRKQTSGNFVKAYIVQ
                     LISMLDMIGGKKLKIVNYILDNVHLSNNTMIATTREIAKATGTSLQTVITTLKILEEGN
                     IIKRKTGVLMLNPELLMRGDDQKQKYLLLEFGNFEQEANEKQENALSDYYSFKD"
                     /name="replication/maintenance protein RepL"
     ARG             667..1400
                     /name="ErmC"
                     /gene="ErmC"
                     /gene_name="Erm 23S ribosomal RNA methyltransferase"
                     /tool="rgi"
                     /drug_class="macrolide antibiotic; lincosamide antibiotic;
                     streptogramin antibiotic; streptogramin A antibiotic;
                     streptogramin B antibiotic"
                     /identity="99.59"
                     /coverage="100.0"
     Typing          1849..2334
                     /name="rep_cluster_1947"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="99.591"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 ttcacataag cgtgcaggtt taaagtacat aaaaaatata atgaaaaaaa gcatcattat
       61 actaacgtta taccaacatt atactctcat tatactaatt gcttattcca atttcctatt
      121 ggttggaacc aacaggcgtt agtgtgttgt tgagttggta ctttcatggg attaatccca
      181 tgaaaccccc aaccaactcg ccaaagcttt ggctaacaca cacgccattc caaccaatag
      241 ttttctcggc ataaagccat gctctgacgc ttaaatgcac taatgcctta aaaaaacatt
      301 aaagtctaac acactagact tatttacttc gtaattaagt cgttaaaccg tgtgctctac
      361 gaccaaaagt ataaaacctt taagaacttt cttttttctt gtaaaaaaag aaactagata
      421 aatctctcat atcttttatt caataatcgc atcagattgc agtataaatt taacgatcac
      481 tcatcatgtt catatttatc agagctcgtg ctataattat actaatttta taaggaggaa
      541 aaaatatggg catttttagt atttttgtaa tcagcacagt tcattatcaa ccaaacaaaa
      601 aataagtggt tataatgaat cgttaataag caaaattcat tataaccaaa ttaaagaggg
      661 ttataatgaa cgagaaaaat ataaaacaca gtcaaaactt tattacttca aaacataata
      721 tagataaaat aatgacaaat ataagattaa atgaacatga taatatcttt gaaatcggct
      781 caggaaaagg gcattttacc cttgaattag tacagaggtg taatttcgta actgccattg
      841 aaatagacca taaattatgc aaaactacag aaaataaact tgttgatcac gataatttcc
      901 aagttttaaa caaggatata ttgcagttta aatttcctaa aaaccaatcc tataaaatat
      961 ttggtaatat accttataac ataagtacgg atataatacg caaaattgtt tttgatagta
     1021 tagctgatga gatttattta atcgtggaat acgggtttgc taaaagatta ttaaatacaa
     1081 aacgctcatt ggcattattt ttaatggcag aagttgatat ttctatatta agtatggttc
     1141 caagagaata ttttcatcct aaacctaaag tgaatagctc acttatcaga ttaaatagaa
     1201 aaaaatcaag aatatcacac aaagataaac agaagtataa ttatttcgtt atgaaatggg
     1261 ttaacaaaga atacaagaaa atatttacaa aaaatcaatt taacaattcc ttaaaacatg
     1321 caggaattga cgatttaaac aatattagct ttgaacaatt cttatctctt ttcaatagct
     1381 ataaattatt taataagtaa gttaagggat gcagtttatg catcccttaa cttgtttttc
     1441 gtgtacctat tttttgtgaa tcgattatgt cttttgcgca ttcacttctt ttctatataa
     1501 atatgagcga agcgaataag cgtcggaaaa gcagcaaaaa gtttcctttt tgctgttgga
     1561 gcatgggggt tcagggggtg cagtatctga cgtcaatgcc gagcgaaagc gagccgaagg
     1621 gtagcattta cgttagataa ccccctgata tgctccgacg ctttatatag aaaagaagat
     1681 tcaactaggt aaaatcttaa tataggttga gatgataagg tttataagga atttgtttgt
     1741 tctaattttt cactcatttt gttctaattt cttttaacaa atgttctttt ttttttagaa
     1801 cagttatgat atagttagaa tagtttaaaa taaggagtga gaaaaagatg aaagaaagat
     1861 atggaacagt ctataaaggc tctcagaggc tcatagacga agaaagtgga gaagtcatag
     1921 aggtagacaa gttataccgt aaacaaacgt ctggtaactt cgtaaaggca tatatagtgc
     1981 aattaataag tatgttagat atgattggcg gaaaaaaact taaaatcgtt aactatatcc
     2041 tagataatgt ccacttaagt aacaatacaa tgatagctac aacaagagaa atagcaaaag
     2101 ctacaggaac aagtctacaa acagtaataa caacacttaa aatcttagaa gaaggaaata
     2161 ttataaaaag aaaaactgga gtattaatgt taaaccctga actactaatg agaggcgacg
     2221 accaaaaaca aaaatacctc ttactcgaat ttgggaactt tgagcaagag gcaaatgaaa
     2281 aacaagaaaa tgcattatct gattattatt ctttcaagga ctagtataac ataaaatcgt
     2341 ctacaaatag acaaaaaacc tgcacgctta atgtagatca aaagcttaac gcaaatgaaa
     2401 tagattgacc tcccaataac accacgtagt tattgggagg tcaatctatg aaatgcgatt
     2461 aagctttttc taa
//
