LOCUS       NZ_CP054448             2276 bp    DNA     circular CON 12-SEP-2023
DEFINITION  Staphylococcus saprophyticus strain UTI-056 plasmid pUTI-056-4,
            complete sequence.
ACCESSION   NZ_CP054448
VERSION     NZ_CP054448.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN15089852
            Assembly: GCF_013341435.1
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  JOURNAL   Unpublished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                   :: 223x
            Sequencing Technology :: Illumina MiSeq, Oxford Nanopore MiniION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 09/12/2023 03:39:11
            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)                      :: 2,539
            Genes (coding)                    :: 2,462
            CDSs (with protein)               :: 2,462
            Genes (RNA)                       :: 83
            rRNAs                             :: 7, 6, 6 (5S, 16S, 23S)
            complete rRNAs                    :: 7, 6, 6 (5S, 16S, 23S)
            tRNAs                             :: 60
            ncRNAs                            :: 4
            Pseudo Genes (total)              :: 77
            CDSs (without protein)            :: 77
            Pseudo Genes (ambiguous residues) :: 0 of 77
            Pseudo Genes (frameshifted)       :: 35 of 77
            Pseudo Genes (incomplete)         :: 32 of 77
            Pseudo Genes (internal stop)      :: 21 of 77
            Pseudo Genes (multiple problems)  :: 10 of 77
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP054448.1.
            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-056"
                     /isolation_source="urine specimens"
                     /host="Homo sapiens"
                     /db_xref="taxon:29385"
                     /plasmid="pUTI-056-4"
                     /geo_loc_name="USA: California"
                     /collection_date="2019"
     gene            59..1063
                     /locus_tag="HSZ51_RS13085"
                     /old_locus_tag="HSZ51_13085"
     CDS             59..1063
                     /locus_tag="HSZ51_RS13085"
                     /old_locus_tag="HSZ51_13085"
                     /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(1690..2013)
                     /gene="qacC"
                     /locus_tag="HSZ51_RS13090"
                     /old_locus_tag="HSZ51_13090"
     ARG             complement(1694..2013)
                     /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(1691..2013)
                     /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          60..1063
                     /name="rep_cluster_1017"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 accccagtag tatgattaaa gcgtctactc aataaacaac tactggaggt ctctttatat
       61 gcaatataat actactagat gtatagacga aaatcaagat aacgaaacac ttaaagatat
      121 gacgaaaagt gggaaacaac gcccatggag agaaaagaag atagataatg taagttatgc
      181 agatatactg gaaattttaa aaataaaaaa ggcttttaat gtaaaacaat gtggtaacgt
      241 cttagagttc aagccgactg atgaaggtta tttgaagtta cataagacat ggttttgtaa
      301 gtcgaaactc tgcccagttt gtaattggag gcgtgctatg aaaaatagtt atcaagctca
      361 aaaagtgatt gaagaagttg ttaaagaaaa accaaaagcg cgttggttat ttttaacact
      421 ttcaacgaaa aatgcgatag atggggatac tttagaacaa agtttgaaac atttaacgaa
      481 agcatttgat aggttaagta gatataaaaa agtgaagcaa aatcttgttg ggtttttgcg
      541 ttcaacggaa gtaacagtta ataaaaatga tggtagttat aatcaacata tgcatgtttt
      601 attatgtgtt gaaaatagtt attttaagaa taaagctaat tatataactc aagaagaatg
      661 ggttaattta tggcaaaaag cattacaagt aaattatcga cccgtagcaa atattaaagc
      721 gatcaaacca aatcaaaaag gcgataaaga tattcaagca gctatcaaag aaacctctaa
      781 atattcggtt aagtcatctg attttttaac tgatgatgat gaaagaaatc aagaaatcgt
      841 gaatgattta gaaaaaggtt tatatcgaaa acgtatgttg agttatggtg gtttgcttaa
      901 acaaaaacat aagattttaa atttagatga tgccgaagat ggcaatttga ttaatacaag
      961 tgacgaagat aaaacaacag acgaagaaga aaaagcacat tcaattacgg caatttggaa
     1021 ttttgaaaaa caaaattatt atttaaaaga tttgaaacgt tagctaaaaa gctagcgttt
     1081 ttttatgtct ttttgcccct gcgggaacta tagcgttcaa ccggcatggt tgaccagttt
     1141 tcatgttaac ttttaagttt gcatgtaaat gggcagtgtt tatttttttc tgcccagttt
     1201 gctaaatttt taatttgcat ataactgggc agtgtctaaa aaattagtca ctggttttgc
     1261 tcaaattttt gtttgtgaaa ttaagatata tttatttggc tcatatttgc gttttaaaag
     1321 cgtatataga cttttaggta taaaactata tgatttaccc ctgaatcttt aaaatgcccc
     1381 cttaaaattc aaataaaggc atataaaaat aaaaagccaa cccagataaa atggattggc
     1441 tttttatttg cttttgcgaa gtagattata aaaaactact tttaataagc accctaaatg
     1501 tgatgtctat attataacaa gaacacgcat ttatgccgag aaaatttatt gtgcgttgag
     1561 aagaaccctt aactaaactt gcagacgaat gtcggcatag cgtgagctat taagccgacc
     1621 attcgacaag ttttgggatt gttaagggtt ccgaggctca acgtcaataa agcaattgga
     1681 ataaagcaat taatgcgatg ttccgaaaat gtttaacgaa actacgccga ctatgattaa
     1741 aactatagat actatagtta ttagatttat ttgttctttg aaaataatta ttgagactac
     1801 ggttgttaag actaaaccta gtcccgccca agttgcataa gttatattta gtggtaggtg
     1861 ttgcattgtt ttacttaaaa aatagaaaca aattccaaat gaaattattg ttcctaagga
     1921 tggtataaat tttgaaaagc cttctgaaga tttaagaaat gcacttccaa taacttcagt
     1981 acttatggct attattaaat aaatataagg catttttaac tccttttaat tttcgtattt
     2041 tatttaattt tattctaagt attttttaat tgtagtcttg tattttgagt gtcattcgcg
     2101 tggtattttt gtggattgat ggtttttgaa aggtttttga aacgagttga aaacgagttt
     2161 cttcttgtct tgatactata tagaaataac tcgattttaa aattatagct gtaatccttg
     2221 gtatgtaagg gattatagct atttttcttg ttgaaaggaa tttttgacat aaaaaa
//
