LOCUS       NZ_CP054835             2276 bp    DNA     circular CON 12-SEP-2023
DEFINITION  Staphylococcus saprophyticus strain UTI-045 plasmid pUTI-045-4,
            complete sequence.
ACCESSION   NZ_CP054835
VERSION     NZ_CP054835.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN15089826
            Assembly: GCF_013358365.1
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  JOURNAL   Unpublished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                   :: 173x
            Sequencing Technology :: Illumina MiSeq, Oxford Nanopore MiniION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 09/12/2023 03:28:10
            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)                     :: 2,741
            CDSs (total)                      :: 2,657
            Genes (coding)                    :: 2,570
            CDSs (with protein)               :: 2,570
            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)              :: 87
            CDSs (without protein)            :: 87
            Pseudo Genes (ambiguous residues) :: 0 of 87
            Pseudo Genes (frameshifted)       :: 41 of 87
            Pseudo Genes (incomplete)         :: 36 of 87
            Pseudo Genes (internal stop)      :: 27 of 87
            Pseudo Genes (multiple problems)  :: 14 of 87
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP054835.1.
            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-045"
                     /isolation_source="urine"
                     /host="Homo sapiens"
                     /db_xref="taxon:29385"
                     /plasmid="pUTI-045-4"
                     /geo_loc_name="USA: California"
                     /collection_date="2019"
     gene            complement(join(1308..2276,1..36))
                     /locus_tag="HSZ48_RS13555"
                     /old_locus_tag="HSZ48_13600"
     CDS             complement(join(1308..2276,1..36))
                     /locus_tag="HSZ48_RS13555"
                     /old_locus_tag="HSZ48_13600"
                     /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            358..681
                     /gene="qacC"
                     /locus_tag="HSZ48_RS13560"
                     /old_locus_tag="HSZ48_13605"
     ARG             359..678
                     /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             359..681
                     /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          complement(1309..2276)
                     /name="rep_cluster_1017"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 attttcgtct atacatctag tagtattata ttgcatataa agagacctcc agtagttgtt
       61 tattgagtag acgctttaat catactactg gggttttttt atgtcaaaaa ttcctttcaa
      121 caagaaaaat agctataatc ccttacatac caaggattac agctataatt ttaaaatcga
      181 gttatttcta tatagtatca agacaagaag aaactcgttt tcaactcgtt tcaaaaacct
      241 ttcaaaaacc atcaatccac aaaaatacca cgcgaatgac actcaaaata caagactaca
      301 attaaaaaat acttagaata aaattaaata aaatacgaaa attaaaagga gttaaaaatg
      361 ccttatattt atttaataat agccataagt actgaagtta ttggaagtgc atttcttaaa
      421 tcttcagaag gcttttcaaa atttatacca tccttaggaa caataatttc atttggaatt
      481 tgtttctatt ttttaagtaa aacaatgcaa cacctaccac taaatataac ttatgcaact
      541 tgggcgggac taggtttagt cttaacaacc gtagtctcaa taattatttt caaagaacaa
      601 ataaatctaa taactatagt atctatagtt ttaatcatag tcggcgtagt ttcgttaaac
      661 attttcggaa catcgcatta attgctttat tccaattgct ttattgacgt tgagcctcgg
      721 aacccttaac aatcccaaaa cttgtcgaat ggtcggctta atagctcacg ctatgccgac
      781 attcgtctgc aagtttagtt aagggttctt ctcaacgcac aataaatttt ctcggcataa
      841 atgcgtgttc ttgttataat atagacatca catttagggt gcttattaaa agtagttttt
      901 tataatctac ttcgcaaaag caaataaaaa gccaatccat tttatctggg ttggcttttt
      961 atttttatat gcctttattt gaattttaag ggggcatttt aaagattcag gggtaaatca
     1021 tatagtttta tacctaaaag tctatatacg cttttaaaac gcaaatatga gccaaataaa
     1081 tatatcttaa tttcacaaac aaaaatttga gcaaaaccag tgactaattt tttagacact
     1141 gcccagttat atgcaaatta aaaatttagc aaactgggca gaaaaaaata aacactgccc
     1201 atttacatgc aaacttaaaa gttaacatga aaactggtca accatgccgg ttgaacgcta
     1261 tagttcccgc aggggcaaaa agacataaaa aaacgctagc tttttagcta acgtttcaaa
     1321 tcttttaaat aataattttg tttttcaaaa ttccaaattg ccgtaattga atgtgctttt
     1381 tcttcttcgt ctgttgtttt atcttcgtca cttgtattaa tcaaattgcc atcttcggca
     1441 tcatctaaat ttaaaatctt atgtttttgt ttaagcaaac caccataact caacatacgt
     1501 tttcgatata aacctttttc taaatcattc acgatttctt gatttctttc atcatcatca
     1561 gttaaaaaat cagatgactt aaccgaatat ttagaggttt ctttgatagc tgcttgaata
     1621 tctttatcgc ctttttgatt tggtttgatc gctttaatat ttgctacggg tcgataattt
     1681 acttgtaatg ctttttgcca taaattaacc cattcttctt gagttatata attagcttta
     1741 ttcttaaaat aactattttc aacacataat aaaacatgca tatgttgatt ataactacca
     1801 tcatttttat taactgttac ttccgttgaa cgcaaaaacc caacaagatt ttgcttcact
     1861 tttttatatc tacttaacct atcaaatgct ttcgttaaat gtttcaaact ttgttctaaa
     1921 gtatccccat ctatcgcatt tttcgttgaa agtgttaaaa ataaccaacg cgcttttggt
     1981 ttttctttaa caacttcttc aatcactttt tgagcttgat aactattttt catagcacgc
     2041 ctccaattac aaactgggca gagtttcgac ttacaaaacc atgtcttatg taacttcaaa
     2101 taaccttcat cagtcggctt gaactctaag acgttaccac attgttttac attaaaagcc
     2161 ttttttattt ttaaaatttc cagtatatct gcataactta cattatctat cttcttttct
     2221 ctccatgggc gttgtttccc acttttcgtc atatctttaa gtgtttcgtt atcttg
//
