LOCUS       NZ_CP054437             2458 bp    DNA     circular CON 12-SEP-2023
DEFINITION  Staphylococcus saprophyticus strain UTI-035 plasmid pUTI-035-3,
            complete sequence.
ACCESSION   NZ_CP054437
VERSION     NZ_CP054437.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN15089825
            Assembly: GCF_013341395.1
KEYWORDS    RefSeq.
SOURCE      Staphylococcus saprophyticus
  ORGANISM  Staphylococcus saprophyticus
            Bacteria; Bacillota; Bacilli; Bacillales; Staphylococcaceae;
            Staphylococcus.
REFERENCE   1  (bases 1 to 2458)
  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  JOURNAL   Unpublished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 2458)
  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                   :: 189x
            Sequencing Technology :: Illumina MiSeq, Oxford Nanopore MiniION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 09/12/2023 03:31:42
            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)                     :: 2,615
            CDSs (total)                      :: 2,534
            Genes (coding)                    :: 2,462
            CDSs (with protein)               :: 2,462
            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)              :: 72
            CDSs (without protein)            :: 72
            Pseudo Genes (ambiguous residues) :: 0 of 72
            Pseudo Genes (frameshifted)       :: 29 of 72
            Pseudo Genes (incomplete)         :: 37 of 72
            Pseudo Genes (internal stop)      :: 20 of 72
            Pseudo Genes (multiple problems)  :: 13 of 72
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP054437.1.
            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..2458
                     /organism="Staphylococcus saprophyticus"
                     /mol_type="genomic DNA"
                     /strain="UTI-035"
                     /isolation_source="urine specimens"
                     /host="Homo sapiens"
                     /db_xref="taxon:29385"
                     /plasmid="pUTI-035-3"
                     /geo_loc_name="USA: California"
                     /collection_date="2019"
     gene            complement(108..308)
                     /locus_tag="HSZ47_RS13020"
     CDS             complement(108..308)
                     /locus_tag="HSZ47_RS13020"
                     /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_142351118.1"
                     /translation="MLKIKYNRIANSQDPSNLNSDDMTWATQLRDILMILEKEEITIEE
                     AIEYLDKVIQNDADDYKNKYL"
                     /name="hypothetical protein"
     gene            complement(547..870)
                     /gene="qacG"
                     /locus_tag="HSZ47_RS13000"
                     /old_locus_tag="HSZ47_13000"
     ARG             complement(548..870)
                     /name="qacG"
                     /gene="qacG"
                     /gene_name="small multidrug resistance (SMR) antibiotic
                     efflux pump"
                     /tool="rgi"
                     /drug_class="disinfecting agents and antiseptics"
                     /identity="91.59"
                     /coverage="100.0"
     gene            1152..2156
                     /locus_tag="HSZ47_RS13005"
                     /old_locus_tag="HSZ47_13005"
     CDS             1152..2156
                     /locus_tag="HSZ47_RS13005"
                     /old_locus_tag="HSZ47_13005"
                     /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_081325143.1"
                     /translation="MQDNHTKYIDENQDNETLKDMTKSGKQRPWREKKIDNVSYADILE
                     ILKIKKAFNVKQCGNVLEFKPTDEGYLKLHKTWFCKSKLCPVCNWRRAMKNSYQAQRVI
                     EEVVKEKPKARWLFLTLSTKNAIDGDTLEQSLNHLTKSFHRLTKYKKVSKNLIGFMRST
                     EVTVNKNDGSYNQHMHVLLCVESKYFRGSENYISQNDWVDLWQKALQVNYRPVANIKAI
                     KPNQKGDKDIQAAIKETSKYSVKSSDFLTDDDEKNQEIVNDLEKGLYRKRMLSYGGLLK
                     QKHKILNLDDVEDGNLINTSDEDKVTDEEEKAHSITAIWNFEKQNYYLKDLKR"
                     /name="protein rep"
     Typing          1167..2156
                     /name="rep_cluster_1017"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="91.927"
                     /coverage="99.0"
                     /evalue="0.0"
ORIGIN
        1 tttaaaatac ccccttaaaa ttcaaaataa aggcatttaa aattcgataa aataaaaagt
       61 ccttagataa aatttctagg gactttttat tttgaatact aaatttgcta tagatattta
      121 tttttgtaat cgtcggcatc gttttgaatg actttatcta aatactcaat agcttcttca
      181 attgttattt cttctttttc taaaatcatt aagatatctc taagttgagt agcccatgtc
      241 atatcatcgc tatttaaatt tgaagggtct tgagaatttg ctatccggtt atattttatt
      301 ttcagcattt ttagtatctc gtcatatggt tttttcaact tatatcatcc ttttattttt
      361 atattaccaa taaagtatta ataacgcatt tatgccgaga aaatttattg atgttgagaa
      421 gaacccttaa ctaaacttgc agacgaatgt cggcatagcg tgagctatta agccgaccat
      481 tcgacaagtt ttgggattgt taagggttcc gaggctcaac gtcaataaag caattggaat
      541 aaattattaa tggctcgttc caaatacatt tagaagtact acgcctataa caattaaacc
      601 gatagaaatg atactaatta aattaacgtt ttctttaaaa ataataactg atactactgt
      661 ggttaatact aatcctaaac ctgcccaggt ggcataagtt atatttagtg gtaaatattt
      721 tattgttaga cttagaaaat aaaaacaaat cccaaatgaa aataatgtac ctaatgttgg
      781 ccataatttt gtgaaacctt ctgatgtttt tagaaaacta gttcctgtta tttctgttgc
      841 aatcgcgata actaaataca aataatgcat taaatttctc ctttgatttt tgtttgataa
      901 tctatatttt aatatagagt aagtgaaaga agaaattatt aagaatttta ttttaaaacg
      961 agttgaaaaa cgagtttttt cttatcttga tactatatag aaataacaat ctttttttat
     1021 attagcttaa aaccttgata tatcagtgtt tcttttgttt tttagtgtat aaaataaaat
     1081 ttgacataaa aaagctccag taataagatt gaagcatcta ctcatcaact taatactgga
     1141 ggtcttttta tatgcaagac aatcatacaa aatatataga cgaaaatcaa gataatgaaa
     1201 cattaaaaga tatgacgaaa agtgggaaac aacgcccatg gagagagaaa aaaattgata
     1261 atgtaagtta tgcagatata ctggaaatct taaaaataaa aaaggctttt aacgtaaaac
     1321 aatgtggtaa cgtcttagaa ttcaagccga ctgatgaagg ttatttgaaa ttacataaga
     1381 catggttttg taagtcgaaa ttatgcccag tttgtaattg gaggcgtgct atgaaaaata
     1441 gttatcaagc tcaacgagtg attgaagaag tcgttaaaga aaagcctaaa gcacgttggt
     1501 tatttttaac actttcaaca aaaaatgcga tagatggaga tactttagaa caaagtttaa
     1561 atcatctaac caagtcattt catagattga ctaagtataa aaaagttagc aaaaatttaa
     1621 ttggttttat gcgttcgact gaggttacag ttaataaaaa tgatggtagt tataatcaac
     1681 atatgcatgt tttattatgt gttgaaagta aatattttag aggttctgag aattatattt
     1741 cacagaatga ttgggtcgat ttatggcaaa aagcattaca agtaaattat cgacctgtcg
     1801 caaatattaa agcgatcaaa ccaaatcaaa aaggtgataa agatattcaa gcagccatca
     1861 aagaaacctc aaaatattcg gttaagtcat ctgatttttt aacggatgat gacgaaaaaa
     1921 atcaagaaat agtgaacgat ttagaaaaag gtttataccg aaaacgtatg ttaagttatg
     1981 gtggattgct taaacaaaaa cataaaattt taaatttaga tgatgtcgaa gatggcaatt
     2041 taattaatac aagtgacgaa gataaagtta cagacgaaga agaaaaagca cattcaatta
     2101 ctgcaatttg gaattttgaa aaacaaaatt attacttaaa agatttaaaa cgttagctca
     2161 aaagctagcg tttttttatg tttttagccc ctgcgggaac tatacgatta accagtatgg
     2221 ttacccagtt tttacgcgaa aaataatttt gtgcgtaact gggcagtgtc tgatttttta
     2281 tgccagtaca tgctaaattt ttaatttgca tgtaaatggg cagtgtctaa aaaatgagtc
     2341 actgatgttg ctcaaatttt tgtttgtgaa attaaaatat atttatttgg ctcatatttg
     2401 cgttttaagc gcttatgtat gtttttaggt ataaaactat ataaattacc cctaaatc
//
