LOCUS       NZ_CP047823             3085 bp    DNA     circular CON 18-DEC-2023
DEFINITION  Staphylococcus aureus strain UP_1278 plasmid unnamed1, complete
            sequence.
ACCESSION   NZ_CP047823
VERSION     NZ_CP047823.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN11175630
            Assembly: GCF_009912195.1
KEYWORDS    RefSeq.
SOURCE      Staphylococcus aureus
  ORGANISM  Staphylococcus aureus
            Bacteria; Bacillota; Bacilli; Bacillales; Staphylococcaceae;
            Staphylococcus.
REFERENCE   1  (bases 1 to 3085)
  AUTHORS   Dilthey,A., Meyer,S. and Kaasch,A.
  TITLE     Increasing the efficiency of long-read sequencing for hybrid
            assembly with k-mer-based multiplexing
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 3085)
  AUTHORS   Dilthey,A., Meyer,S. and Kaasch,A.
  TITLE     Direct Submission
  JOURNAL   Submitted (14-JAN-2020) Institute for Medical Microbiology and
            Hospital Hygene, University Hospital Duesseldorf, Moorenstrasse 5,
            Duesseldorf 40225, Germany
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method :: Unicycler Hybrid Assembly v. 0.4.8
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 43x / 446x
            Sequencing Technology :: Illumina MiSeq / Oxford Nanopore MiniION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 12/17/2023 03:56:23
            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)                     :: 2,814
            CDSs (total)                      :: 2,732
            Genes (coding)                    :: 2,647
            CDSs (with protein)               :: 2,647
            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)              :: 85
            CDSs (without protein)            :: 85
            Pseudo Genes (ambiguous residues) :: 0 of 85
            Pseudo Genes (frameshifted)       :: 47 of 85
            Pseudo Genes (incomplete)         :: 39 of 85
            Pseudo Genes (internal stop)      :: 19 of 85
            Pseudo Genes (multiple problems)  :: 18 of 85
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP047823.1.
            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..3085
                     /organism="Staphylococcus aureus"
                     /mol_type="genomic DNA"
                     /strain="UP_1278"
                     /host="Homo sapiens"
                     /db_xref="taxon:1280"
                     /plasmid="unnamed1"
     gene            join(2654..3085,1..489)
                     /locus_tag="E3T02_RS14025"
                     /old_locus_tag="E3T02_14025"
     CDS             join(2654..3085,1..489)
                     /locus_tag="E3T02_RS14025"
                     /old_locus_tag="E3T02_14025"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_002445662.1"
                     /GO_function="GO:0003677 - DNA binding [Evidence IEA]"
                     /GO_process="GO:0006260 - DNA replication [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="protein rep"
                     /protein_id="WP_011274352.1"
                     /translation="MDKYTEKKQRNQVFQKFIERHVKEGQMDLIRECNTFLSFVSDKTL
                     EKQKLYKSNLCKNRFCPVCAWRKARKDALGLSLMMQYIKQKEDKQFIFLTLTTPNVTVE
                     HLEDEIKHYNESFRRLSNRKHFKSIAKGYVRKLEITYNKKRDDYNPHFHVLIAVNKSYF
                     TDKRYYISQKEWLELWRDVTGNQAITQVHVQKVKQNNNKELYEMAKYSGKDSDYLVNQK
                     VFDAFYKALKGKQVLVYSGLFKDARKKLKNGELDYLKESDPTEYIYQIFYVWNQKEYLA
                     SEIYDLTEEEKREVNNQMINEIEEE"
                     /name="protein rep"
     gene            complement(1364..1756)
                     /locus_tag="E3T02_RS14030"
                     /old_locus_tag="E3T02_14030"
     CDS             complement(1364..1756)
                     /locus_tag="E3T02_RS14030"
                     /old_locus_tag="E3T02_14030"
                     /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="hypothetical protein"
                     /protein_id="WP_031824197.1"
                     /translation="MENTNNLFERLEILTKPENIETTFFIILKFIIFIIILMIGALIVL
                     GILNSRRNYNPEKIWNKRKIRTLKSEIGGGQEYYFRYWIWQRNKRKNILIALRDYSPYE
                     EYYPSQKWLKKDKSKLPFRREIWVIK"
                     /name="hypothetical protein"
     gene            complement(1967..2290)
                     /gene="qacC"
                     /locus_tag="E3T02_RS14035"
                     /old_locus_tag="E3T02_14035"
     ARG             complement(1971..2290)
                     /name="qacC"
                     /gene="qacC"
                     /gene_name="quaternary ammonium compound efflux SMR
                     transporter QacC"
                     /tool="amrfinderplus"
                     /drug_class="QUATERNARY AMMONIUM"
                     /identity="99.07"
                     /coverage="100.0"
     ARG             complement(1968..2290)
                     /name="qacJ"
                     /gene="qacJ"
                     /gene_name="small multidrug resistance (SMR) antibiotic
                     efflux pump"
                     /tool="rgi"
                     /drug_class="disinfecting agents and antiseptics"
                     /identity="72.9"
                     /coverage="100.0"
     Typing          2..484
                     /name="rep_cluster_1281"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="82.062"
                     /coverage="99.0"
                     /evalue="3.25e-112"
     Typing          2655..3085
                     /name="rep_cluster_1300"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          2..486
                     /name="MOBC"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="83.333"
                     /coverage="97.0"
                     /evalue="1.49e-88"
ORIGIN
        1 cgcgatgatt ataatccaca ttttcatgta ttaattgcgg ttaataaatc atattttaca
       61 gataagcgat attatataag ccaaaaagaa tggcttgaac tatggcgtga tgtgacaggt
      121 aatcaagcta ttacacaagt tcatgttcaa aaggttaagc aaaacaataa taaagaactt
      181 tatgaaatgg ctaaatattc cggtaaagat agcgattatc tcgttaatca aaaagtattc
      241 gacgcatttt ataaagcatt aaaaggcaaa caggtacttg tctattctgg attgtttaaa
      301 gatgcacgca aaaagctaaa aaatggcgag ttggattatc tcaaagaaag tgatccgaca
      361 gaatatattt accaaatctt ttatgtgtgg aatcaaaaag agtatctagc aagtgagatt
      421 tacgacttaa ccgaagaaga aaaacgagaa gtaaacaacc aaatgattaa cgaaattgaa
      481 gaagagtaaa aagacgttag cgaaagctag cgtctttttt attccaattt gccttatggt
      541 ttggaaccaa caaggcttat tgtgttgttg agttggtact ttcttgggat taatcccaaa
      601 tcaagaccaa ccaactctct agaatgaatc tagctaacac aaaatctatt ccaaacaata
      661 agttttctcg gcataaaagg tgttgtgatt ttgaattgaa ttagtgggcg attttgataa
      721 agtgcaaacc cttttcggta acccactttt tgagttaaaa aggggtagtg caggattaag
      781 agttgatatc caactcgtga aaagcactgt tgtgcttggt tttgacctga ttttgctttc
      841 cacttttagt gatttcgaaa atctataata cttgatatga aaggctttat ggtgatttaa
      901 ggcgattaaa atcgaaaagg ggtttgcact taactttgcg gtaaattttc ggtggttttg
      961 tatttggctc atatttgcgt tttaagagct tatataagtt tttaggcata aaactatatg
     1021 aattacccct aaatctttaa aatgccccct taaaattcaa aataaaggta tttaaaattt
     1081 taaaaataaa aaagctacta gcaaaaaact agtagcttaa atcttagtta aattttgatg
     1141 tagtattaat ttttatatct acgctacaac gtcgattcaa attcgtgcag tattaatttt
     1201 tgtatctgcg ccacaacgcc gattacttaa aactaagata aaaaatcgac gaaggtcgat
     1261 tatggttttt gcacgcgttc tttttagaac gcataagtgc gcccttacgg gatttaacta
     1321 gattataacg atgaaaaata gacatgtaaa gtaagaaggt tagttatttt ataacccata
     1381 tttctcttcg gaatggtaat ttagatttat ctttttttag ccatttttga cttggataat
     1441 attcttcata tggagagtaa tctcttaaag cgattagaat attttttctt ttatttcttt
     1501 gccagatcca gtatctaaaa tagtattcct gtcctccgcc aatttctgat ttaagagtgc
     1561 gaatttttct tttgttccaa attttttcag ggttgtaatt tcttctgcta ttcaatattc
     1621 ctaaaactat taacgctcct atcattagaa tgatgataaa aataatgaat ttaaggataa
     1681 taaaaaatgt agtttctata ttttctggtt ttgttaatat ttctaatctt tcgaatagat
     1741 tattagtgtt ttccaactac tatcacctcg aaatagtatt tattgcttat ttttgattat
     1801 atcgcattta tgccgagaaa atttattgtg cgttgagaag aacccttaac taaacttgca
     1861 gacgaatgtc ggcatagcgt gagctattaa gccgaccatt cgacaagttt tgggattgtt
     1921 aagggttccg aggctcaacg tcaataaagc aattggaata aagcaattaa tgcgatgttc
     1981 cgaaaatgtt taacaaaact acgccgacta tgattaaaac tatagatact atagttatta
     2041 gatttatttg ttctttgaaa ataattattg agactacggt tgttaagact aaacctagtc
     2101 ccgcccaagt tgcataagtt atatttagtg gtaggtgttg cattgtttta cttaaaaaat
     2161 agaaacaaat tccaaatgaa attattgttc ctaaggatgg tataaatttt gaaaagcctt
     2221 ctgaagattt aagaaatgca cttccaataa cttcagtact tatggctatt attaaataaa
     2281 tataaggcat ttttaactcc ttttaatttt cgtattttat ttaattttat tctaagtatt
     2341 ttttaattgt agtcttgtat tttgagtgtc attcgcgtgg tatttttgtg gattgatggt
     2401 ttttgaaagg tttttgaaac gagttgaaaa cgagtttctt cttgtcttga tactataggt
     2461 aactattaca agctacgata gttaccttta atctgttggt atatctggtt tcgagcgcaa
     2521 aaaaagttgc tttttcgtac ctagtatagt agagtttatg gtgtccaagc caaaacttta
     2581 caagaaagga gaaaaagcaa cttttttatg gcattagttt gtataaaact aagttgtttt
     2641 gttgtgttat aacatggata agtatactga gaagaaacaa agaaatcaag tatttcagaa
     2701 atttattgaa cgacatgtca aagaaggaca aatggatttg ataagggagt gtaatacatt
     2761 cttgagtttt gtgtcagata agacgttaga aaaacagaaa ttgtataaat ctaatttgtg
     2821 taaaaatcga ttttgtcctg tatgtgcatg gcgaaaagcg agaaaagatg cgttaggttt
     2881 atcattgatg atgcaatata ttaagcaaaa ggaagataaa caattcatct ttttaacact
     2941 tacgacgcca aatgtaacag ttgagcattt ggaagatgaa ataaaacatt ataatgagtc
     3001 gtttagacga ttaagtaatc gtaaacactt taaatctata gctaaaggtt acgtaagaaa
     3061 attagaaatc acttataaca aaaaa
//
