LOCUS       NZ_CP054443             2276 bp    DNA     circular CON 12-SEP-2023
DEFINITION  Staphylococcus saprophyticus strain UTI-058y plasmid pUTI-058y-3,
            complete sequence.
ACCESSION   NZ_CP054443
VERSION     NZ_CP054443.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN15089863
            Assembly: GCF_013341455.1
KEYWORDS    RefSeq.
SOURCE      Staphylococcus saprophyticus
  ORGANISM  Staphylococcus saprophyticus
            Bacteria; Bacillota; Bacilli; Bacillales; Staphylococcaceae;
            Staphylococcus.
REFERENCE   1  (bases 1 to 2276)
  AUTHORS   Stephens,C., Wright,M., Hartman,A., Gonzales,A., Sensabaugh,G.,
            Robinson,P., Lopez,G. and Hess,D.
  TITLE     Complete genome sequences of diverse uropathogenic Staphylococcus
            saprophyticus isolates from a college health center
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 2276)
  AUTHORS   Stephens,C., Wright,M., Hartman,A., Gonzales,A., Sensabaugh,G.,
            Robinson,P., Lopez,G. and Hess,D.
  TITLE     Direct Submission
  JOURNAL   Submitted (03-JUN-2020) Biology, Santa Clara University, 500 El
            Camino Real, Santa Clara, CA 95054, USA
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: Unicycler v. 0.4.8
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 200x
            Sequencing Technology :: Illumina MiSeq, Oxford Nanopore MiniION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 09/12/2023 03:36:52
            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)                     :: 2,622
            CDSs (total)                      :: 2,541
            Genes (coding)                    :: 2,465
            CDSs (with protein)               :: 2,465
            Genes (RNA)                       :: 81
            rRNAs                             :: 7, 6, 6 (5S, 16S, 23S)
            complete rRNAs                    :: 7, 6, 6 (5S, 16S, 23S)
            tRNAs                             :: 58
            ncRNAs                            :: 4
            Pseudo Genes (total)              :: 76
            CDSs (without protein)            :: 76
            Pseudo Genes (ambiguous residues) :: 0 of 76
            Pseudo Genes (frameshifted)       :: 35 of 76
            Pseudo Genes (incomplete)         :: 31 of 76
            Pseudo Genes (internal stop)      :: 21 of 76
            Pseudo Genes (multiple problems)  :: 10 of 76
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP054443.1.
            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..2276
                     /organism="Staphylococcus saprophyticus"
                     /mol_type="genomic DNA"
                     /strain="UTI-058y"
                     /isolation_source="urine specimens"
                     /host="Homo sapiens"
                     /db_xref="taxon:29385"
                     /plasmid="pUTI-058y-3"
                     /geo_loc_name="USA: California"
                     /collection_date="2019"
     gene            65..1069
                     /locus_tag="HSZ52_RS13025"
                     /old_locus_tag="HSZ52_13025"
     CDS             65..1069
                     /locus_tag="HSZ52_RS13025"
                     /old_locus_tag="HSZ52_13025"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_020368559.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="protein rep"
                     /protein_id="WP_001199882.1"
                     /translation="MQYNTTRCIDENQDNETLKDMTKSGKQRPWREKKIDNVSYADILE
                     ILKIKKAFNVKQCGNVLEFKPTDEGYLKLHKTWFCKSKLCPVCNWRRAMKNSYQAQKVI
                     EEVVKEKPKARWLFLTLSTKNAIDGDTLEQSLKHLTKAFDRLSRYKKVKQNLVGFLRST
                     EVTVNKNDGSYNQHMHVLLCVENSYFKNKANYITQEEWVNLWQKALQVNYRPVANIKAI
                     KPNQKGDKDIQAAIKETSKYSVKSSDFLTDDDERNQEIVNDLEKGLYRKRMLSYGGLLK
                     QKHKILNLDDAEDGNLINTSDEDKTTDEEEKAHSITAIWNFEKQNYYLKDLKR"
                     /name="protein rep"
     gene            complement(1696..2019)
                     /gene="qacC"
                     /locus_tag="HSZ52_RS13030"
                     /old_locus_tag="HSZ52_13030"
     ARG             complement(1700..2019)
                     /name="qacC"
                     /gene="qacC"
                     /gene_name="quaternary ammonium compound efflux SMR
                     transporter QacC"
                     /tool="amrfinderplus"
                     /drug_class="QUATERNARY AMMONIUM"
                     /identity="100.0"
                     /coverage="100.0"
     ARG             complement(1697..2019)
                     /name="qacJ"
                     /gene="qacJ"
                     /gene_name="small multidrug resistance (SMR) antibiotic
                     efflux pump"
                     /tool="rgi"
                     /drug_class="disinfecting agents and antiseptics"
                     /identity="71.96"
                     /coverage="100.0"
     Typing          66..1069
                     /name="rep_cluster_1017"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 aaaaaaaccc cagtagtatg attaaagcgt ctactcaata aacaactact ggaggtctct
       61 ttatatgcaa tataatacta ctagatgtat agacgaaaat caagataacg aaacacttaa
      121 agatatgacg aaaagtggga aacaacgccc atggagagaa aagaagatag ataatgtaag
      181 ttatgcagat atactggaaa ttttaaaaat aaaaaaggct tttaatgtaa aacaatgtgg
      241 taacgtctta gagttcaagc cgactgatga aggttatttg aagttacata agacatggtt
      301 ttgtaagtcg aaactctgcc cagtttgtaa ttggaggcgt gctatgaaaa atagttatca
      361 agctcaaaaa gtgattgaag aagttgttaa agaaaaacca aaagcgcgtt ggttattttt
      421 aacactttca acgaaaaatg cgatagatgg ggatacttta gaacaaagtt tgaaacattt
      481 aacgaaagca tttgataggt taagtagata taaaaaagtg aagcaaaatc ttgttgggtt
      541 tttgcgttca acggaagtaa cagttaataa aaatgatggt agttataatc aacatatgca
      601 tgttttatta tgtgttgaaa atagttattt taagaataaa gctaattata taactcaaga
      661 agaatgggtt aatttatggc aaaaagcatt acaagtaaat tatcgacccg tagcaaatat
      721 taaagcgatc aaaccaaatc aaaaaggcga taaagatatt caagcagcta tcaaagaaac
      781 ctctaaatat tcggttaagt catctgattt tttaactgat gatgatgaaa gaaatcaaga
      841 aatcgtgaat gatttagaaa aaggtttata tcgaaaacgt atgttgagtt atggtggttt
      901 gcttaaacaa aaacataaga ttttaaattt agatgatgcc gaagatggca atttgattaa
      961 tacaagtgac gaagataaaa caacagacga agaagaaaaa gcacattcaa ttacggcaat
     1021 ttggaatttt gaaaaacaaa attattattt aaaagatttg aaacgttagc taaaaagcta
     1081 gcgttttttt atgtcttttt gcccctgcgg gaactatagc gttcaaccgg catggttgac
     1141 cagttttcat gttaactttt aagtttgcat gtaaatgggc agtgtttatt tttttctgcc
     1201 cagtttgcta aatttttaat ttgcatataa ctgggcagtg tctaaaaaat tagtcactgg
     1261 ttttgctcaa atttttgttt gtgaaattaa gatatattta tttggctcat atttgcgttt
     1321 taaaagcgta tatagacttt taggtataaa actatatgat ttacccctga atctttaaaa
     1381 tgccccctta aaattcaaat aaaggcatat aaaaataaaa agccaaccca gataaaatgg
     1441 attggctttt tatttgcttt tgcgaagtag attataaaaa actactttta ataagcaccc
     1501 taaatgtgat gtctatatta taacaagaac acgcatttat gccgagaaaa tttattgtgc
     1561 gttgagaaga acccttaact aaacttgcag acgaatgtcg gcatagcgtg agctattaag
     1621 ccgaccattc gacaagtttt gggattgtta agggttccga ggctcaacgt caataaagca
     1681 attggaataa agcaattaat gcgatgttcc gaaaatgttt aacgaaacta cgccgactat
     1741 gattaaaact atagatacta tagttattag atttatttgt tctttgaaaa taattattga
     1801 gactacggtt gttaagacta aacctagtcc cgcccaagtt gcataagtta tatttagtgg
     1861 taggtgttgc attgttttac ttaaaaaata gaaacaaatt ccaaatgaaa ttattgttcc
     1921 taaggatggt ataaattttg aaaagccttc tgaagattta agaaatgcac ttccaataac
     1981 ttcagtactt atggctatta ttaaataaat ataaggcatt tttaactcct tttaattttc
     2041 gtattttatt taattttatt ctaagtattt tttaattgta gtcttgtatt ttgagtgtca
     2101 ttcgcgtggt atttttgtgg attgatggtt tttgaaaggt ttttgaaacg agttgaaaac
     2161 gagtttcttc ttgtcttgat actatataga aataactcga ttttaaaatt atagctgtaa
     2221 tccttggtat gtaagggatt atagctattt ttcttgttga aaggaatttt tgacat
//
