LOCUS       NZ_CP069472             3125 bp    DNA     circular CON 08-MAY-2024
DEFINITION  Staphylococcus aureus strain FDAARGOS_1246 plasmid unnamed2,
            complete sequence.
ACCESSION   NZ_CP069472
VERSION     NZ_CP069472.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN16357388
            Assembly: GCF_016889145.1
KEYWORDS    RefSeq.
SOURCE      Staphylococcus aureus
  ORGANISM  Staphylococcus aureus
            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  JOURNAL   Unpublished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
            Genome Coverage                   :: 2103.49x
            Sequencing Technology             :: Pacbio; Illumina
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_016889145.1-RS_2024_05_06
            Annotation Date                   :: 05/06/2024 11:28:22
            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)                     :: 2,911
            CDSs (total)                      :: 2,829
            Genes (coding)                    :: 2,743
            CDSs (with protein)               :: 2,743
            Genes (RNA)                       :: 82
            rRNAs                             :: 7, 6, 6 (5S, 16S, 23S)
            complete rRNAs                    :: 7, 6, 6 (5S, 16S, 23S)
            tRNAs                             :: 59
            ncRNAs                            :: 4
            Pseudo Genes (total)              :: 86
            CDSs (without protein)            :: 86
            Pseudo Genes (ambiguous residues) :: 0 of 86
            Pseudo Genes (frameshifted)       :: 47 of 86
            Pseudo Genes (incomplete)         :: 43 of 86
            Pseudo Genes (internal stop)      :: 20 of 86
            Pseudo Genes (multiple problems)  :: 23 of 86
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP069472.1.
            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 aureus"
                     /mol_type="genomic DNA"
                     /strain="FDAARGOS_1246"
                     /culture_collection="FDA:FDAARGOS_1246"
                     /db_xref="taxon:1280"
                     /plasmid="unnamed2"
                     /geo_loc_name="USA: MD"
                     /collected_by="FDA-Stanford Microbiome Effort"
     gene            complement(326..514)
                     /locus_tag="I6J76_RS14510"
                     /old_locus_tag="I6J76_14510"
     CDS             complement(326..514)
                     /locus_tag="I6J76_RS14510"
                     /old_locus_tag="I6J76_14510"
                     /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"
     gene            complement(1097..2092)
                     /locus_tag="I6J76_RS14515"
                     /old_locus_tag="I6J76_14515"
     CDS             complement(1097..2092)
                     /locus_tag="I6J76_RS14515"
                     /old_locus_tag="I6J76_14515"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001199895.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /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            2544..3125
                     /locus_tag="I6J76_RS14520"
                     /old_locus_tag="I6J76_14520"
     CDS             2544..3125
                     /locus_tag="I6J76_RS14520"
                     /old_locus_tag="I6J76_14520"
                     /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"
     Typing          complement(863..1027)
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="2.42e-81"
     Typing          complement(1098..2092)
                     /name="rep_cluster_1017"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="99.9"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 atactattta ttccaattgc tttattgacg ttgagcctcg gaacccttaa caatcccaaa
       61 acttgtcgaa tggtcggctt aatagctcac gctatgccga cattcgtctg caagtttagt
      121 taagggttct tctcaacatc aataaatttt ctcggcataa atgcgtcgtc tattttttat
      181 tatcttcatg ataatcatat ttttcttcca tctcgtcaaa agcatcatct ttatagaaaa
      241 acaaaaagta agcaacaaca ccaataggaa taaaaaaaca gtgtgaaaac aagaagaaac
      301 tcgtttcaaa atcccctcaa atattctaat tattcttttt gaaattcata accttaacaa
      361 ccaaataaat agcatttatt cccatcaaaa taacatacgg aattaatata tataaatttt
      421 ccaaatgaga tataaaaatt aatccaagta aaaagaaaac atttaaaata gttgctataa
      481 cgtaaccttc atctaacact gtgtttttat tcaaaataaa cactcctttt ttaaaaaact
      541 ttatcacaag acttactcaa attataaata cctttatttt gagttttaag ggggtatttt
      601 aaaggtttag ggggtatcat ataggttttt aacttaaaaa tatatacaag ctcttaaaac
      661 gcaaatatga gccaaataaa tatatggtaa tttcacaaac aaaaatttca gcaaaaccag
      721 tgactaattt tttaacactg cccatttaca tgcaaattaa aaattagcat aaaatccttt
      781 aaaacttcca catgtttttc taaattcctg cagggcgttt tttatcaaaa atcgagaatt
      841 tttaattttt ctctaaaaac tccgtaagag cataaggaga atttgctatc attcaaaaat
      901 gataggtctg gcaaagccag aaattccagg ggttttaagg tattttaaag tgatatcata
      961 caaagctgta ctgtcttatt tttgtgacac aatatattgc gtttgtctta tttttgtgac
     1021 actacataca gcatttgtca caaaaataag acagtacttt tttataaaaa atcaacaaaa
     1081 aagacattag tcaacactaa tgtcttaaat aataattttg cttttcgaaa ttccaaattg
     1141 cggtaattga atgtgctttt tcttcttcgt ctgttgtttt atcttcatca cttgcattaa
     1201 tcaaattacc atcttcgaca tcgtctaagt ttaaaatttt atgtttttgt ttaagcaatc
     1261 caccataact taacatacgt tttcgataca aacctttttc taaatcactt acaatttctt
     1321 gatttttttc atcatcatca gttaaaaaat cagatgattt aaccgaatat tttgaggtct
     1381 ctttgattgc cgattcaatg tctttatcgc cttttctatt cggtttgatc gctttaacat
     1441 tagcaacagg tcgatagtca acttgtaatg ctctttgcca taaattaacc cattcttctt
     1501 gagttatata attctctttt tttctaaaat atgcattttc aacacataac aaaacatgca
     1561 tgtgctgatt ataactaccg tcatttttat taacggtaac ttctgttgaa cgcataaatc
     1621 caacaagatt ttgtttaacc tttttatatc tactcaacct atcaaatgct ttagttagat
     1681 gcttcaaact ttgttctaaa gtatctccat ctatcgcatt ttttgttgaa agtgttaaaa
     1741 acaaccaacg tgcttttggc ttttccttaa ttactttttc aatcactttt tgagcttgat
     1801 aactattttt catagcacgt ctccaattac aaaccggaca taattttgat ttacaaaacc
     1861 atgtcttatg taacttcaaa tagccttcat cagttggctt aaattctaaa atattaccac
     1921 attgttttac attaaaagcc tttttgattt ttaaaatttc tagtatatct gcatagctta
     1981 cattatctat tttcttttct ctccatgggc gttgtttccc acttttcgtc atatctttta
     2041 acgttttatt atcttgattt tcggttatac ttctagtagt attatattgc atataaaaag
     2101 acccccagta ttatttaaga ttcgacacct taataatata actggggttt tttattgtca
     2161 aattttcctt tcacgcacaa aaacacgttt aaacactgta atatcaacag ttacagctat
     2221 atatataaaa tcgagttatt tctatatagt atcaagacaa gaagaaactc gttcacactc
     2281 gtttcaaaaa acaacctatt ccttcttctt tttatgaccc tctaaaccta aataaattaa
     2341 tgtgaaaacc aatgaataaa taaaactttc taaaaagtca aaaggattat caaataaaat
     2401 cgaattaaca aaattaaaaa ttaaaaatac agataataaa ataatcaaaa agtaaaaaaa
     2461 cttattcata ttaaactcct ttgtttttat atgttaatat tatattgaat tcatttaaat
     2521 aacaaaacaa gggggcattt acaatgaatg caattcaaaa cagtatatca ctaagaaaga
     2581 ttttagtagt atctttaagt attttaacca tactttcaat ggtcttggat tttaatttca
     2641 aagaagctca agcccaaaac aaaaataaca ttgcagataa aaacgttgaa actttaaacg
     2701 aaaaagaaat tgaaaaagaa ctaaaataca tatatggcaa aattattatt ttagataaag
     2761 acggaacagc taaagatgtt aatctagaaa atgccaaatc tcgatatgga tatgttcctg
     2821 aaggattcca aaaactaaaa aacgacatag agaataaaaa gaaaactagt tcaatatcac
     2881 ctagagcagt tggtgggaac tacaaaaata gcggtgactg tttctattct gaagttttaa
     2941 actcatatgg agaactttta actggaaaca taatcacagc agtttttgaa gatgttaaag
     3001 ccaaaaactt aaagggcgta gcaaaaaaat tagctaaaat tgggataaaa ggaaacctag
     3061 ctggaatcgc agctactatg gtttcgaagg atgtacaatg taatcttaaa tacgggttac
     3121 tttag
//
