LOCUS       NZ_CP069950             2366 bp    DNA     circular CON 02-APR-2024
DEFINITION  Staphylococcus epidermidis strain FDAARGOS_1363 plasmid unnamed3,
            complete sequence.
ACCESSION   NZ_CP069950
VERSION     NZ_CP069950.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN16357505
            Assembly: GCF_016903555.1
KEYWORDS    RefSeq.
SOURCE      Staphylococcus epidermidis
  ORGANISM  Staphylococcus epidermidis
            Bacteria; Bacillota; Bacilli; Bacillales; Staphylococcaceae;
            Staphylococcus.
REFERENCE   1  (bases 1 to 2366)
  AUTHORS   Carlson,P., Fischbach,M., Hastie,J., Bilen,M., Cheng,A., 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  JOURNAL   Unpublished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 2366)
  AUTHORS   Carlson,P., Fischbach,M., Hastie,J., Bilen,M., Cheng,A., 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 (05-FEB-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
            Genome Coverage                   :: 1898.18x
            Sequencing Technology             :: Pacbio; Illumina
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_016903555.1-RS_2024_04_02
            Annotation Date                   :: 04/02/2024 04:37:36
            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)                     :: 2,421
            CDSs (total)                      :: 2,337
            Genes (coding)                    :: 2,275
            CDSs (with protein)               :: 2,275
            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)              :: 62
            CDSs (without protein)            :: 62
            Pseudo Genes (ambiguous residues) :: 0 of 62
            Pseudo Genes (frameshifted)       :: 32 of 62
            Pseudo Genes (incomplete)         :: 38 of 62
            Pseudo Genes (internal stop)      :: 21 of 62
            Pseudo Genes (multiple problems)  :: 23 of 62
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP069950.1.
            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_1363"
                     /culture_collection="FDA:FDAARGOS_1363"
                     /db_xref="taxon:1282"
                     /plasmid="unnamed3"
                     /geo_loc_name="USA: MD"
                     /collected_by="FDA-Stanford Microbiome Effort"
     gene            25..759
                     /gene="erm(C)"
                     /locus_tag="I6K93_RS00005"
                     /old_locus_tag="I6K93_00005"
     ARG             26..756
                     /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            1207..1683
                     /locus_tag="I6K93_RS00010"
                     /old_locus_tag="I6K93_00010"
     CDS             1207..1683
                     /locus_tag="I6K93_RS00010"
                     /old_locus_tag="I6K93_00010"
                     /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             2..759
                     /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="99.18"
                     /coverage="103.28"
     Typing          1208..1693
                     /name="rep_cluster_1947"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="99.591"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 gaggaaaaaa taaagagggt tataatgaac gagaaaaata taaaacacag tcaaaacttt
       61 attacttcaa aacataatat agataaaata atgacaaata taagattaaa tgaacatgat
      121 aatatctttg aaatcggctc aggaaaaggg cattttaccc ttgaattagt acagaggtgt
      181 aatttcgtaa ctgccattga aatagaccat aaattatgca aaactacaga aaataaactt
      241 gttgatcacg ataatttcca agttttaaac aaggatatat tgcagtttaa atttcctaaa
      301 aaccaatcct ataaaatatt tggtaatata ccttataaca taagtacgga tataatacgc
      361 aaaattgttt ttgatagtat agctgatgag atttatttaa tcgtggaata cgagtttgct
      421 aaaagattat taaatacaaa acgctcattg gcattatttt taatggcaga agttgatatt
      481 tctatattaa gtatggttcc aagagaatat tttcatccta aacctaaagt gaatagctca
      541 cttatcagat taaatagaaa aaaatcaaga atatcacaca aagataaaca gaagtataat
      601 tatttcgtta tgaaatgggt taacaaagaa tacaagaaaa tatttacaaa aaatcaattt
      661 aacaattcct taaaacatgc aggaattgac gatttaaaca atattagctt tgaacaattc
      721 ttatctcttt tcaatagcta taaattattt aataagtaag ttaagggatg cataaactgc
      781 atcccttaac ttgtttttcg tgtacctatt ttttgtgaat cgattatgtc ttttgcgcat
      841 tcacttcttt tctatataaa tatgagcgaa gcgaataagc gtcggaaaag cagcaaaaag
      901 tttccttttt gctgttggag catgggggtt cagggggtgc agtatctgac gtcaatgccg
      961 agcgaaagcg agccgaaggg tagcatttac gttagataac cccctgatat gctccgacgc
     1021 tttatataga aaagaagatt caactaggta aaatcttaat ataggttgag atgataaggt
     1081 ttataaggaa tttgtttgtt ctaatttttc actcattttg ttctaatttc ttttaacaaa
     1141 tgttcttttt tttttagaac agttatgata tagttagaat agtttaaaat aaggagtgag
     1201 aaaaagatga aagaaagata tggaacagtc tataaaggct ctcagaggct catagacgaa
     1261 gaaagtggag aagtcataga ggtagacaag ttataccgta aacaaacgtc tggtaacttc
     1321 gtaaaggcat atatagtgca attaataagt atgttagata tgattggcgg aaaaaaactt
     1381 aaaatcgtta actatatcct agataatgtc cacttaagta acaatacaat gatagctaca
     1441 acaagagaaa tagcaaaagc tacaggaaca agtctacaaa cagtaataac aacacttaaa
     1501 atcttagaag aaggaaatat tataaaaaga aaaactggag tattaatgtt aaaccctgaa
     1561 ctactaatga gaggcgacga ccaaaaacaa aaatacctct tactcgaatt tgggaacttt
     1621 gagcaagagg caaatgaaaa acaagaaaat gcattatctg attattattc tttcaaggac
     1681 tagtataaca taaaatcgtc tacaaataga caaaaaacct gcacgcttaa tgtagatcaa
     1741 aagcttaacg caaatgaaat agattgacct cccaataaca ccacgtagtt attgggaggt
     1801 caatctatga aatgcgatta agctttttct aattcacata agcgtgcagg tttaaagtac
     1861 ataaaaaata taatgaaaaa aagcatcatt atactaacgt tataccaaca ttatactctc
     1921 attatactaa ttgcttattc caatttccta ttggttggaa ccaacaggcg ttagtgtgtt
     1981 gttgagttgg tactttcatg ggattaatcc catgaaaccc ccaaccaact cgccaaagct
     2041 ttggctaaca cacacgccat tccaaccaat agttttctcg gcataaagcc atgctctgac
     2101 gcttaaatgc actaatgcct taaaaaaaca ttaaagtcta acacactaga cttatttact
     2161 tcgtaattaa gtcgttaaac cgtgtgctct acgaccaaaa gtataaaacc tttaagaact
     2221 ttcttttttc ttgtaaaaaa agaaactaga taaatctctc atatctttta ttcaataatc
     2281 gcatcagatt gcagtataaa tttaacgatc actcatcatg ttcatattta tcagagctcg
     2341 tgctataatt atactaattt tataag
//
