LOCUS       NZ_CP069479             3125 bp    DNA     circular CON 02-APR-2024
DEFINITION  Staphylococcus epidermidis strain FDAARGOS_1243 plasmid unnamed6,
            complete sequence.
ACCESSION   NZ_CP069479
VERSION     NZ_CP069479.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN16357385
            Assembly: GCF_016889165.1
KEYWORDS    RefSeq.
SOURCE      Staphylococcus epidermidis
  ORGANISM  Staphylococcus epidermidis
            Bacteria; Bacillota; Bacilli; Bacillales; Staphylococcaceae;
            Staphylococcus.
REFERENCE   1  (bases 1 to 3125)
  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  JOURNAL   Unpublished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 3125)
  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, SPAdes v. 3.14.1
            Genome Coverage                   :: 3182.86x
            Sequencing Technology             :: Pacbio; Illumina
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_016889165.1-RS_2024_04_02
            Annotation Date                   :: 04/02/2024 04:37:37
            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)                     :: 2,447
            CDSs (total)                      :: 2,363
            Genes (coding)                    :: 2,300
            CDSs (with protein)               :: 2,300
            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)       :: 34 of 63
            Pseudo Genes (incomplete)         :: 37 of 63
            Pseudo Genes (internal stop)      :: 22 of 63
            Pseudo Genes (multiple problems)  :: 24 of 63
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP069479.1.
            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..3125
                     /organism="Staphylococcus epidermidis"
                     /mol_type="genomic DNA"
                     /strain="FDAARGOS_1243"
                     /culture_collection="FDA:FDAARGOS_1243"
                     /db_xref="taxon:1282"
                     /plasmid="unnamed6"
                     /geo_loc_name="USA: MD"
                     /collected_by="FDA-Stanford Microbiome Effort"
     gene            complement(join(2548..3125,1..418))
                     /locus_tag="I6J73_RS12175"
                     /old_locus_tag="I6J73_12180"
     CDS             complement(join(2548..3125,1..418))
                     /locus_tag="I6J73_RS12175"
                     /old_locus_tag="I6J73_12180"
                     /inference="COORDINATES: ab initio prediction:GeneMarkS-2+"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GeneMarkS-2+."
                     /codon_start=1
                     /transl_table=11
                     /product="protein rep"
                     /protein_id="WP_001199892.1"
                     /translation="MQYNTTRSITENQDNKTLKDMTKSGKQRPWREKKIDNVSYADILE
                     ILKIKKAFNVKQCGNILEFKPTDEGYLKLHKTWFCKSKLCPVCNWRRAMKNSYQAQKVI
                     EKVIKEKPKARWLFLTLSTKNAIDGDTLEQSLKHLTKAFDRLSRYKKVKQNLVGFMRST
                     EVTVNKNDGSYNQHMHVLLCVENAYFRKKENYITQEEWVNLWQRALQVDYRPVANVKAI
                     KPNRKGDKDIESAIKETSKYSVKSSDFLTDDDEKNQEIVSDLEKGLYRKRMLSYGGLLK
                     QKHKILNLDDVEDGNLINASDEDKTTDEEEKAHSITAIWNFEKQNYYLRH"
                     /name="protein rep"
     gene            870..1451
                     /locus_tag="I6J73_RS12180"
                     /old_locus_tag="I6J73_12185"
     CDS             870..1451
                     /locus_tag="I6J73_RS12180"
                     /old_locus_tag="I6J73_12185"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000991705.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_000991705.1"
                     /translation="MNAIQNSISLRKILVVSLSILTILSMVLDFNFKEAQAQNKNNIAD
                     KNVETLNEKEIEKELKYIYGKIIILDKDGTAKDVNLENAKSRYGYVPEGFQKLKNDIEN
                     KKKTSSISPRAVGGNYKNSGDCFYSEVLNSYGELLTGNIITAVFEDVKAKNLKGVAKKL
                     AKIGIKGNLAGIAATMVSKDVQCNLKYGLL"
                     /name="hypothetical protein"
     gene            complement(1621..1743)
                     /locus_tag="I6J73_RS12375"
     CDS             complement(1621..1743)
                     /locus_tag="I6J73_RS12375"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000491229.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_000491229.1"
                     /translation="MFSHCFFIPIGVVAYFLFFYKDDAFDEMEEKYDYHEDNKK"
                     /name="hypothetical protein"
     gene            complement(1777..1965)
                     /locus_tag="I6J73_RS12185"
                     /old_locus_tag="I6J73_12190"
     CDS             complement(1777..1965)
                     /locus_tag="I6J73_RS12185"
                     /old_locus_tag="I6J73_12190"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001030810.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_001039248.1"
                     /translation="MNKNTVLDEGYVIATILNVFFLLGLIFISHLENLYILIPYVILMG
                     INAIYLVVKVMNFKKNN"
                     /name="hypothetical protein"
     Typing          complement(2314..2478)
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="2.42e-81"
     Typing          complement(2..418)
                     /name="rep_cluster_1017"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          complement(2551..3123)
                     /name="rep_cluster_1017"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="89.721"
                     /coverage="99.0"
                     /evalue="0.0"
ORIGIN
        1 ttagatgctt caaactttgt tctaaagtat ctccatctat cgcatttttt gttgaaagtg
       61 ttaaaaacaa ccaacgtgct tttggctttt ccttaattac tttttcaatc actttttgag
      121 cttgataact atttttcata gcacgtctcc aattacaaac cggacataat tttgatttac
      181 aaaaccatgt cttatgtaac ttcaaatagc cttcatcagt tggcttaaat tctaaaatat
      241 taccacattg ttttacatta aaagcctttt tgatttttaa aatttctagt atatctgcat
      301 agcttacatt atctattttc ttttctctcc atgggcgttg tttcccactt ttcgtcatat
      361 cttttaacgt tttattatct tgattttcgg ttatacttct agtagtatta tattgcatat
      421 aaaaagaccc ccagtattat ttaagattcg acaccttaat aatataactg gggtttttta
      481 ttgtcaaatt ttcctttcac gcacaaaaac acgtttaaac actgtaatat caacagttac
      541 agctatatat ataaaatcga gttatttcta tatagtatca agacaagaag aaactcgttc
      601 acactcgttt caaaaaacaa cctattcctt cttcttttta tgaccctcta aacctaaata
      661 aattaatgtg aaaaccaatg aataaataaa actttctaaa aagtcaaaag gattatcaaa
      721 taaaatcgaa ttaacaaaat taaaaattaa aaatacagat aataaaataa tcaaaaagta
      781 aaaaaactta ttcatattaa actcctttgt ttttatatgt taatattata ttgaattcat
      841 ttaaataaca aaacaagggg gcatttacaa tgaatgcaat tcaaaacagt atatcactaa
      901 gaaagatttt agtagtatct ttaagtattt taaccatact ttcaatggtc ttggatttta
      961 atttcaaaga agctcaagcc caaaacaaaa ataacattgc agataaaaac gttgaaactt
     1021 taaacgaaaa agaaattgaa aaagaactaa aatacatata tggcaaaatt attattttag
     1081 ataaagacgg aacagctaaa gatgttaatc tagaaaatgc caaatctcga tatggatatg
     1141 ttcctgaagg attccaaaaa ctaaaaaacg acatagagaa taaaaagaaa actagttcaa
     1201 tatcacctag agcagttggt gggaactaca aaaatagcgg tgactgtttc tattctgaag
     1261 ttttaaactc atatggagaa cttttaactg gaaacataat cacagcagtt tttgaagatg
     1321 ttaaagccaa aaacttaaag ggcgtagcaa aaaaattagc taaaattggg ataaaaggaa
     1381 acctagctgg aatcgcagct actatggttt cgaaggatgt acaatgtaat cttaaatacg
     1441 ggttacttta gatactattt attccaattg ctttattgac gttgagcctc ggaaccctta
     1501 acaatcccaa aacttgtcga atggtcggct taatagctca cgctatgccg acattcgtct
     1561 gcaagtttag ttaagggttc ttctcaacat caataaattt tctcggcata aatgcgtcgt
     1621 ctatttttta ttatcttcat gataatcata tttttcttcc atctcgtcaa aagcatcatc
     1681 tttatagaaa aacaaaaagt aagcaacaac accaatagga ataaaaaaac agtgtgaaaa
     1741 caagaagaaa ctcgtttcaa aatcccctca aatattctaa ttattctttt tgaaattcat
     1801 aaccttaaca accaaataaa tagcatttat tcccatcaaa ataacatacg gaattaatat
     1861 atataaattt tccaaatgag atataaaaat taatccaagt aaaaagaaaa catttaaaat
     1921 agttgctata acgtaacctt catctaacac tgtgttttta ttcaaaataa acactccttt
     1981 tttaaaaaac tttatcacaa gacttactca aattataaat acctttattt tgagttttaa
     2041 gggggtattt taaaggttta gggggtatca tataggtttt taacttaaaa atatatacaa
     2101 gctcttaaaa cgcaaatatg agccaaataa atatatggta atttcacaaa caaaaatttc
     2161 agcaaaacca gtgactaatt ttttaacact gcccatttac atgcaaatta aaaattagca
     2221 taaaatcctt taaaacttcc acatgttttt ctaaattcct gcagggcgtt ttttatcaaa
     2281 aatcgagaat ttttaatttt tctctaaaaa ctccgtaaga gcataaggag aatttgctat
     2341 cattcaaaaa tgataggtct ggcaaagcca gaaattccag gggttttaag gtattttaaa
     2401 gtgatatcat acaaagctgt actgtcttat ttttgtgaca caatatattg cgtttgtctt
     2461 atttttgtga cactacatac agcatttgtc acaaaaataa gacagtactt ttttataaaa
     2521 aatcaacaaa aaagacatta gtcaacacta atgtcttaaa taataatttt gcttttcgaa
     2581 attccaaatt gcggtaattg aatgtgcttt ttcttcttcg tctgttgttt tatcttcatc
     2641 acttgcatta atcaaattac catcttcgac atcgtctaag tttaaaattt tatgtttttg
     2701 tttaagcaat ccaccataac ttaacatacg ttttcgatac aaaccttttt ctaaatcact
     2761 tacaatttct tgattttttt catcatcatc agttaaaaaa tcagatgatt taaccgaata
     2821 ttttgaggtc tctttgattg ccgattcaat gtctttatcg ccttttctat tcggtttgat
     2881 cgctttaaca ttagcaacag gtcgatagtc aacttgtaat gctctttgcc ataaattaac
     2941 ccattcttct tgagttatat aattctcttt ttttctaaaa tatgcatttt caacacataa
     3001 caaaacatgc atgtgctgat tataactacc gtcattttta ttaacggtaa cttctgttga
     3061 acgcataaat ccaacaagat tttgtttaac ctttttatat ctactcaacc tatcaaatgc
     3121 tttag
//
