LOCUS       NZ_CP033783             2366 bp    DNA     circular CON 17-JUL-2023
DEFINITION  Staphylococcus epidermidis strain FDAARGOS_529 plasmid unnamed2,
            complete sequence.
ACCESSION   NZ_CP033783
VERSION     NZ_CP033783.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN10163224
            Assembly: GCF_003812425.1
KEYWORDS    RefSeq.
SOURCE      Staphylococcus epidermidis
  ORGANISM  Staphylococcus epidermidis
            Bacteria; Bacillota; Bacilli; Bacillales; Staphylococcaceae;
            Staphylococcus.
REFERENCE   1  (bases 1 to 2366)
  AUTHORS   Campos,J., Goldberg,B., Tallon,L., Sadzewicz,L., Zhao,X.,
            Vavikolanu,K., Mehta,A., Aluvathingal,J., Nadendla,S., Geyer,C.,
            Nandy,P., 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  JOURNAL   Unpublished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 2366)
  AUTHORS   Campos,J., Goldberg,B., Tallon,L., Sadzewicz,L., Zhao,X.,
            Vavikolanu,K., Mehta,A., Aluvathingal,J., Nadendla,S., Geyer,C.,
            Nandy,P., Yan,Y. and Sichtig,H.
  TITLE     Direct Submission
  JOURNAL   Submitted (13-NOV-2018) Center for Devices and Radiological Health,
            US Food and Drug Administration, 10903 New Hampshire Avenue, Silver
            Spring, MD 20993-0002, USA
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method :: SMRT v. 2.3.0, HGAP v. 3.0, SPAdes v. 3.6.0
            Genome Coverage                   :: 2140.01391846154x
            Sequencing Technology             :: PacBio; Illumina
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 07/17/2023 01:40:27
            Annotation Pipeline :: NCBI Prokaryotic Genome Annotation Pipeline
            (PGAP)
            Annotation Method :: Best-placed reference protein set; GeneMarkS-2+
            Annotation Software revision      :: 6.5
            Features Annotated                :: Gene; CDS; rRNA; tRNA; ncRNA
            Genes (total)                     :: 2,476
            CDSs (total)                      :: 2,392
            Genes (coding)                    :: 2,314
            CDSs (with protein)               :: 2,314
            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)              :: 78
            CDSs (without protein)            :: 78
            Pseudo Genes (ambiguous residues) :: 0 of 78
            Pseudo Genes (frameshifted)       :: 43 of 78
            Pseudo Genes (incomplete)         :: 48 of 78
            Pseudo Genes (internal stop)      :: 33 of 78
            Pseudo Genes (multiple problems)  :: 32 of 78
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP033783.1.
            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..2366
                     /organism="Staphylococcus epidermidis"
                     /mol_type="genomic DNA"
                     /strain="FDAARGOS_529"
                     /isolation_source="CVP line blood"
                     /host="Homo sapiens"
                     /culture_collection="FDA:FDAARGOS_529"
                     /db_xref="taxon:1282"
                     /plasmid="unnamed2"
                     /collection_date="2016-03-24"
                     /collected_by="Children's National Hospital"
     gene            complement(618..1094)
                     /locus_tag="EGX64_RS12745"
                     /old_locus_tag="EGX64_12740"
     CDS             complement(618..1094)
                     /locus_tag="EGX64_RS12745"
                     /old_locus_tag="EGX64_12740"
                     /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"
     gene            complement(1542..2276)
                     /gene="erm(C)"
                     /locus_tag="EGX64_RS12750"
                     /old_locus_tag="EGX64_12745"
     ARG             complement(1546..2276)
                     /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"
     ARG             complement(1543..2276)
                     /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          complement(609..1094)
                     /name="rep_cluster_1947"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="99.591"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 tttatactgc aatctgatgc gattattgaa taaaagatat gagagattta tctagtttct
       61 ttttttacaa gaaaaaagaa agttcttaaa ggttttatac ttttggtcgt agagcacacg
      121 gtttaacgac ttaattacga agtaaataag tctagtgtgt tagactttaa tgttttttta
      181 aggcattagt gcatttaagc gtcagagcat ggctttatgc cgagaaaact attggttgga
      241 atggcgtgtg tgttagccaa agctttggcg agttggttgg gggtttcatg ggattaatcc
      301 catgaaagta ccaactcaac aacacactaa cgcctgttgg ttccaaccaa taggaaattg
      361 gaataagcaa ttagtataat gagagtataa tgttggtata acgttagtat aatgatgctt
      421 tttttcatta tattttttat gtactttaaa cctgcacgct tatgtgaatt agaaaaagct
      481 taatcgcatt tcatagattg acctcccaat aactacgtgg tgttattggg aggtcaatct
      541 atttcatttg cgttaagctt ttgatctaca ttaagcgtgc aggttttttg tctatttgta
      601 gacgatttta tgttatacta gtccttgaaa gaataataat cagataatgc attttcttgt
      661 ttttcatttg cctcttgctc aaagttccca aattcgagta agaggtattt ttgtttttgg
      721 tcgtcgcctc tcattagtag ttcagggttt aacattaata ctccagtttt tctttttata
      781 atatttcctt cttctaagat tttaagtgtt gttattactg tttgtagact tgttcctgta
      841 gcttttgcta tttctcttgt tgtagctatc attgtattgt tacttaagtg gacattatct
      901 aggatatagt taacgatttt aagttttttt ccgccaatca tatctaacat acttattaat
      961 tgcactatat atgcctttac gaagttacca gacgtttgtt tacggtataa cttgtctacc
     1021 tctatgactt ctccactttc ttcgtctatg agcctctgag agcctttata gactgttcca
     1081 tatctttctt tcatcttttt ctcactcctt attttaaact attctaacta tatcataact
     1141 gttctaaaaa aaaaagaaca tttgttaaaa gaaattagaa caaaatgagt gaaaaattag
     1201 aacaaacaaa ttccttataa accttatcat ctcaacctat attaagattt tacctagttg
     1261 aatcttcttt tctatataaa gcgtcggagc atatcagggg gttatctaac gtaaatgcta
     1321 cccttcggct cgctttcgct cggcattgac gtcagatact gcaccccctg aacccccatg
     1381 ctccaacagc aaaaaggaaa ctttttgctg cttttccgac gcttattcgc ttcgctcata
     1441 tttatataga aaagaagtga atgcgcaaaa gacataatcg attcacaaaa aataggtaca
     1501 cgaaaaacaa gttaagggat gcagtttatg catcccttaa cttacttatt aaataattta
     1561 tagctattga aaagagataa gaattgttca aagctaatat tgtttaaatc gtcaattcct
     1621 gcatgtttta aggaattgtt aaattgattt tttgtaaata ttttcttgta ttctttgtta
     1681 acccatttca taacgaaata attatacttc tgtttatctt tgtgtgatat tcttgatttt
     1741 tttctattta atctgataag tgagctattc actttaggtt taggatgaaa atattctctt
     1801 ggaaccatac ttaatataga aatatcaact tctgccatta aaaataatgc caatgagcgt
     1861 tttgtattta ataatctttt agcaaacccg tattccacga ttaaataaat ctcatcagct
     1921 atactatcaa aaacaatttt gcgtattata tccgtactta tgttataagg tatattacca
     1981 aatattttat aggattggtt tttaggaaat ttaaactgca atatatcctt gtttaaaact
     2041 tggaaattat cgtgatcaac aagtttattt tctgtagttt tgcataattt atggtctatt
     2101 tcaatggcag ttacgaaatt acacctctgt actaattcaa gggtaaaatg cccttttcct
     2161 gagccgattt caaagatatt atcatgttca tttaatctta tatttgtcat tattttatct
     2221 atattatgtt ttgaagtaat aaagttttga ctgtgtttta tatttttctc gttcattata
     2281 accctcttta ttttttcctc cttataaaat tagtataatt atagcacgag ctctgataaa
     2341 tatgaacatg atgagtgatc gttaaa
//
