LOCUS       NZ_CP034012             3011 bp    DNA     circular CON 11-FEB-2024
DEFINITION  Staphylococcus aureus strain P1D1C1 plasmid unnamed1, complete
            sequence.
ACCESSION   NZ_CP034012
VERSION     NZ_CP034012.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN10374685
            Assembly: GCF_009739845.1
KEYWORDS    RefSeq.
SOURCE      Staphylococcus aureus
  ORGANISM  Staphylococcus aureus
            Bacteria; Bacillota; Bacilli; Bacillales; Staphylococcaceae;
            Staphylococcus.
REFERENCE   1  (bases 1 to 3011)
  AUTHORS   Liu,J., Gefen,O., Ronin,I., Bar-Meir,M. and Balaban,N.Q.
  TITLE     Rapid evolution of tolerance in patients infected with S. aureus
            promotes antibiotic resistance
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 3011)
  AUTHORS   Liu,J., Gefen,O., Ronin,I., Bar-Meir,M. and Balaban,N.Q.
  TITLE     Direct Submission
  JOURNAL   Submitted (15-NOV-2018) Racah Institute of Physics, Hebrew
            University, Givat ram, Jerusalem 91904, Israel
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: Celera Assembler v. 1.7
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 400x
            Sequencing Technology             :: PacBio + Illumina HiSeq
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 02/11/2024 02:55:03
            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)                     :: 2,805
            CDSs (total)                      :: 2,723
            Genes (coding)                    :: 2,641
            CDSs (with protein)               :: 2,641
            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)              :: 82
            CDSs (without protein)            :: 82
            Pseudo Genes (ambiguous residues) :: 0 of 82
            Pseudo Genes (frameshifted)       :: 46 of 82
            Pseudo Genes (incomplete)         :: 36 of 82
            Pseudo Genes (internal stop)      :: 30 of 82
            Pseudo Genes (multiple problems)  :: 28 of 82
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP034012.1.
            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..3011
                     /organism="Staphylococcus aureus"
                     /mol_type="genomic DNA"
                     /strain="P1D1C1"
                     /isolation_source="blood"
                     /host="Homo sapiens"
                     /db_xref="taxon:1280"
                     /plasmid="unnamed1"
                     /geo_loc_name="Israel: Jerusalem"
                     /lat_lon="31.7732 N 35.1853 E"
                     /collection_date="2017-05-04"
                     /collected_by="Shaare Zedek"
     gene            complement(453..1448)
                     /locus_tag="EFD67_RS00005"
                     /old_locus_tag="EFD67_00010"
     CDS             complement(453..1448)
                     /locus_tag="EFD67_RS00005"
                     /old_locus_tag="EFD67_00010"
                     /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_001199895.1"
                     /translation="MQYNTTRSITENQDNKTLKDMTKSGKQRPWREKKIDNVSYADILE
                     ILKIKKAYNVKQCGNVLEFKPTDEGYLKLHKTWFCKSKLCPVCNWRRAMKNSYQAQKVI
                     EEVIKEKPKARWLFLTLSTKNAIDGDTLEQSLKHLTKAFDRLSRYKKVKQNLVGFMRST
                     EVTVNKNDGSYNQHMHVLLCVENAYFRKKENYITQEEWVNLWQKALQVDYRPVANIKAI
                     KPNQKGDKDIESAIKETSKYSVKSSDFLTDNDEKNQEIVSDLEKGLYRKRMLSYGGLLK
                     QKHKILNLDDAEDGNLINTSDEDKITDEEAKAHSITAIWNFEKQNYYLRH"
                     /name="protein rep"
     gene            1900..2481
                     /locus_tag="EFD67_RS00010"
                     /old_locus_tag="EFD67_00015"
     CDS             1900..2481
                     /locus_tag="EFD67_RS00010"
                     /old_locus_tag="EFD67_00015"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000991701.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_000991701.1"
                     /translation="MNAIQKSVSLRKVLVISLSFLTILSMVLNFNFKEAQAQNKNNIAD
                     KNIETLNEKEIEKELDYIYGKIIVLDKDGTAKDVNLENAKSRYGYVPEGFQKLKNDIEN
                     KKKNSSISPRAVGGNYKNSNDCFYSEVLNSYGELLTGNIIAAVFDDVKAKNIKSAAKKL
                     ARIGIKGNLAGIAATMVSKDVQCTLKYGWF"
                     /name="hypothetical protein"
     Typing          complement(219..383)
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="99.398"
                     /coverage="100.0"
                     /evalue="1.13e-79"
     Typing          complement(454..1448)
                     /name="rep_cluster_1017"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="96.687"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 aaatatgagc caaataaata tattctgatt ttataatcaa aaatttttta taatcaaaaa
       61 ttcgatcaaa cccagtgtcg atttttcgga cactgcccat ttacatgcaa attaaaaatt
      121 agcataaaat cctttaaaac ttcccccatg tttttctaaa ttcctgcagg gcgcttttta
      181 tcaaaaatcg agaattttta atttttctct aagaactccg taagagcata aggagaattt
      241 gctatcattc aaaaatgata ggtctggcaa agccagacat tccaagggtt ttaagtaatt
      301 ttaaagtgat atcataaaaa gctgtagtgt cacacttttg tgacacaata tattgcgttt
      361 gtcacagttt tgtgacacta catacagcat ttgtcacaaa aataagacag tactttttta
      421 caaaaaatca ataaaaaaga catcagtcat cactaatgtc ttaaataata attttgtttt
      481 tcaaaattcc aaattgccgt aattgaatgt gcttttgctt cttcatctgt tattttatct
      541 tcatcacttg tattaattaa attaccatct tcagcatcgt ctaagtttaa aattttatgc
      601 ttttgtttaa gcaatccacc ataacttaac atacgttttc gatataaacc tttttctaaa
      661 tcacttacaa tttcttgatt tttttcgtca ttgtcagtta aaaaatcaga tgacttaacc
      721 gaatattttg atgtctcttt gattgccgat tcaatatctt tatcgccttt ttgattaggt
      781 ttaattgctt taatatttgc aacaggtcga taatcaactt gtaatgcttt ttgccataaa
      841 ttaacccatt cttcttgagt tatataattc tctttttttc taaaatatgc attttcaaca
      901 cataacaaaa cgtgcatatg ctgattataa ctaccatcat ttttattaac ggtaacttct
      961 gttgaacgca taaatccaac aagattttgt ttaacctttt tatatctact caacctatca
     1021 aatgctttag ttagatgctt caaactttgt tctaaagtat ctccatctat cgcatttttg
     1081 gttgaaagtg ttaaaaacaa ccaacgtgct tttggctttt ccttaattac ttcttcaatc
     1141 actttttgag cttgataact atttttcata gcacgcctcc aattacaaac tggacatagc
     1201 tttgatttac aaaaccacgt cttatgtaat ttcaaataac cttcatcggt cggcttgaat
     1261 tctaagacgt taccacattg ttttacgtta taagcctttt ttatttttaa aatttcaagt
     1321 atatctgcat agcttacatt atctattttc ttttctctcc atgggcgttg tttcccactt
     1381 ttcgtcatat cttttaacgt tttattatct tgattttcgg ttatacttct agtagtatta
     1441 tattgcatat aaaaagaccc ccagtattat ttaagattcg acaccttaat aatataactg
     1501 gggtttttta ttgtcaaatt ttcctttcac gcacaaaaac acgtttaaac gctgtaatat
     1561 caacagttac agctatatat ataaaatcga gttatttcta tatagtatca agacaagaag
     1621 aaactcgttt tcaactcgtt tcaaaaacaa tctatttctt tttctcttta tagccctcta
     1681 aacctaaata aatcaatgtg aaaaccaacg aataaataaa gctttctaaa aagtcaaaag
     1741 gattattaaa taaaatcgaa ttaacaaaat taaatattaa aaatacggac aataaaacaa
     1801 ttaaaaaata aataaactta ttcatattaa actcctttgt ttttatatgt taatattata
     1861 ttggattcat ttaaataaca aaacaagggg gcatttataa tgaatgcaat tcaaaaaagt
     1921 gtatcactaa gaaaagtttt agtaatatct ttaagttttt taactatact ttcaatggtc
     1981 ttgaatttta attttaaaga agctcaagcc caaaacaaaa acaacatcgc agataaaaac
     2041 attgaaactt taaacgaaaa agaaatcgaa aaagaactag actacatata tggcaaaatt
     2101 attgttttag ataaagacgg aaccgctaaa gatgttaatc tagaaaatgc caaatctaga
     2161 tatggatatg ttcctgaagg tttccaaaaa ctaaagaacg acatagagaa taaaaagaaa
     2221 aatagctcaa tatcacctag agcagttggt ggaaactaca aaaatagtaa tgactgtttc
     2281 tattctgaag ttttaaactc atatggagaa cttttaaccg gtaatataat cgcagcagtt
     2341 tttgatgatg taaaagccaa aaacataaag agtgcagcaa aaaaattagc cagaattggc
     2401 ataaaaggaa atttagctgg aattgcagct actatggttt caaaggatgt acaatgtact
     2461 ctgaaatacg gatggttcta aatatataat ttattccaat tgctttattg acgttgagcc
     2521 tcggaaccct taacaatccc taaacttgtc gaatcgtcgg cttaatagct cacgctatgc
     2581 cgacattcgt cttcaagttt agttaagggt tcttctcaac atcaataaat tttctcggca
     2641 taaatgcatg tttgattatg cgtgtaacta tcccttaaat aaaacattaa ttgtgcactg
     2701 atttactaat tattatccct tgctttcatt cacactataa tcaacacctt aattctaaac
     2761 atctgaagta atcataattt ttaaacctaa taaaattcgt gactatctta gttaaactct
     2821 gtttaattaa gattttttat ttttcgttat ccaagaggcg catttacata cttaaaaatg
     2881 cgtcgagcta aaaccaaaat ttacgtgtaa taatcgaata tacttatttt gcattttaag
     2941 ggggtattta gaacgaactt taaaaatata tagttttata cctgtattat cttatttgtt
     3001 tcttaaaacg c
//
