LOCUS       NZ_CP132560             4439 bp    DNA     circular CON 24-AUG-2023
DEFINITION  Staphylococcus saprophyticus strain SZ.YL11 plasmid pSZ.YL11,
            complete sequence.
ACCESSION   NZ_CP132560
VERSION     NZ_CP132560.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN36970824
            Assembly: GCF_030845335.1
KEYWORDS    RefSeq.
SOURCE      Staphylococcus saprophyticus
  ORGANISM  Staphylococcus saprophyticus
            Bacteria; Bacillota; Bacilli; Bacillales; Staphylococcaceae;
            Staphylococcus.
REFERENCE   1  (bases 1 to 4439)
  AUTHORS   Zhang,S.Q., Leung,K.M., Lai,G.K.K. and Griffin,S.D.J.
  TITLE     Complete genome sequence of Staphylococcus saprophyticus subsp.
            saprophyticus YL11, recovered from a human fingertip
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 4439)
  AUTHORS   Zhang,S.Q., Leung,K.M., Lai,G.K.K. and Griffin,S.D.J.
  TITLE     Direct Submission
  JOURNAL   Submitted (13-AUG-2023) Shuyuan Molecular Biology Laboratory, The
            Independent Schools Foundation Academy, 1 Kong Sin Wan Road,
            Pokfulam, Hong Kong HK SAR, Hong Kong
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Date                     :: 16-MAY-2023
            Assembly Method                   :: Unicycler v. v0.4.8-beta
            Assembly Name :: SarahZ_AMR_YL11_Novo04_11_49Flow_9_S_sapr ophyticus
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 405.0x
            Sequencing Technology :: Illumina NovaSeq; Oxford Nanopore MinION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 08/21/2023 16:29:27
            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)                     :: 2,581
            CDSs (total)                      :: 2,498
            Genes (coding)                    :: 2,429
            CDSs (with protein)               :: 2,429
            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)              :: 69
            CDSs (without protein)            :: 69
            Pseudo Genes (ambiguous residues) :: 0 of 69
            Pseudo Genes (frameshifted)       :: 28 of 69
            Pseudo Genes (incomplete)         :: 33 of 69
            Pseudo Genes (internal stop)      :: 26 of 69
            Pseudo Genes (multiple problems)  :: 14 of 69
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP132560.1.
            Bacteria and source DNA available from Dr. Simon D. J. Griffin,
            Shuyuan Molecular Biology Laboratory, The ISF Academy, 1 Kong Sin
            Wan Road, Pokfulam, Hong Kong.
            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..4439
                     /organism="Staphylococcus saprophyticus"
                     /mol_type="genomic DNA"
                     /strain="SZ.YL11"
                     /isolation_source="fingertip"
                     /host="Homo sapiens"
                     /db_xref="taxon:29385"
                     /plasmid="pSZ.YL11"
                     /geo_loc_name="Hong Kong: Telegraph Bay"
                     /lat_lon="22.2642601 N 114.1299767 E"
                     /collection_date="2022-11-16"
                     /collected_by="Sarah S. Q. Zhang"
     gene            join(3474..4439,1..276)
                     /gene="mobV"
                     /locus_tag="RA085_RS12895"
                     /old_locus_tag="RA085_12890"
     CDS             join(3474..4439,1..276)
                     /gene="mobV"
                     /locus_tag="RA085_RS12895"
                     /old_locus_tag="RA085_12890"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_010889940.1"
                     /GO_function="GO:0003677 - DNA binding [Evidence IEA]"
                     /GO_process="GO:0006310 - DNA recombination [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MobV family relaxase"
                     /protein_id="WP_000122374.1"
                     /translation="MSYSIVRVSKVKSGTNTTGIQKHVQRENNNYENEDIDHSKTYLNY
                     DLVNANKQNFNNLIDEKIEQNYTGKRKIRTDAIKHIDGLITSDNDFFDNQTPEDTKQFF
                     EYAKEFLEQEYGKDNLLYATVHMDEKTPHMHYGVVPITDDGRLSAKEVVGNKKALTAFQ
                     DRFNEHVKQRGYDLERGQSRQVTNAKHEQISQYKQKTEYHKQEYERESQKTDHIKQKND
                     KLMQEYQKSLNTLKKPINVPYEQETEKVGGLFSKEIQETGNVVISQKDFNEFQKQIKAA
                     QDISEDYEYIKSGRALDDKDKEIREKDDLLNKAVERIENADDNFNQLYENAKPLKENIE
                     IALKLLKILLKELERVLGRNTFAERVNKLTEDEPKLNGLAGNLDKKMNPELYSEQEQQQ
                     EQQKNQKRDRGMHL"
                     /name="mobV"
     gene            803..1747
                     /locus_tag="RA085_RS12900"
                     /old_locus_tag="RA085_12895"
     CDS             803..1747
                     /locus_tag="RA085_RS12900"
                     /old_locus_tag="RA085_12895"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000277654.1"
                     /GO_function="GO:0003677 - DNA binding [Evidence IEA];
                     GO:0003916 - DNA topoisomerase activity [Evidence IEA]"
                     /GO_process="GO:0006270 - DNA replication initiation
                     [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="replication initiation factor domain-containing
                     protein"
                     /protein_id="WP_000277654.1"
                     /translation="MYKNNHANHSNHLENHDLDNFSKTGYSNSRLDAHTVCISDPKLSF
                     DAMTIVGNLNRDNAQALSKFMSVEPQIRLWDILQTKFKAKALQEKVYIEYDKVKADSWD
                     RRNMRIEFNPNKLTRDEMIWLKQNIISYMEDDGFTRLDLAFDFEDDLSDYYAMSDKAVK
                     KTIFYGRNGKPETKYFGVRDSNRFIRIYNKKQERKDNADAEVMSEHLWRVEIELKRDMV
                     DYWNDCFSDLHILQPDWKTIQRTADRAIVFMLLSDEEEWGKLHRNSRTKYKNLIKEISP
                     VDLTDLMKSTLKANEKQLQKQIDFWQHEFKFWK"
                     /name="replication initiation factor domain-containing
                     protein"
     gene            1909..3288
                     /gene="tet(K)"
                     /locus_tag="RA085_RS12905"
                     /old_locus_tag="RA085_12900"
     ARG             1910..3285
                     /name="tet(K)"
                     /gene="tet(K)"
                     /gene_name="tetracycline efflux MFS transporter Tet(K)"
                     /tool="amrfinderplus"
                     /drug_class="TETRACYCLINE"
                     /identity="100.0"
                     /coverage="100.0"
     Typing          804..1747
                     /name="rep_cluster_1118"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          3475..4439
                     /name="MOBV"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 gataatttta accaacttta cgaaaatgca aagccactta aagagaatat agaaatagcg
       61 ttaaagcttt taaaaatctt actaaaagag ttagaacgag ttttaggaag aaataccttt
      121 gcggaaagag ttaataagtt aacagaagat gaaccaaaac taaatggttt agcaggaaac
      181 ttagataaaa aaatgaatcc agaattatat tcagaacagg aacagcaaca agaacaacaa
      241 aagaatcaaa aacgagatag aggtatgcac ttatagaaca tgcatttatg ccgagaaaac
      301 ttattggttg gaatgggcta tgtgttagct aacttgttag cgagttggtt ggacttgaat
      361 tgggattaat cccaagaaag taccaactca acaacacata aagccctgta ggttccgacc
      421 aataaggaaa ttggaataaa gcaataaaag gagttgaaga aatgaaattc agagaagcct
      481 ttgagaattt tataacaagt aagtatgtac ttggtgtttt agtagtttta actgtttacc
      541 agataataca aatgcttaaa taaaaaaaga cttgatctga ttagaccaag tcttttgata
      601 gtgttatatt aataacaaaa taaaaaggag tcgctcacgc cctgaccaaa gtttgtgaac
      661 gacatcattc aaagaaaaaa acactgagtt gtttttataa tcttgtatat ttagatatta
      721 aacgatattt aaatatacat caagatatat atttgggtga gcgattcctt aaacgaaatt
      781 gagattaagg agtcgatttt ttatgtataa aaacaatcat gcaaatcatt caaatcattt
      841 ggaaaatcac gatttagaca atttttctaa aaccggctac tctaatagcc ggttggacgc
      901 acatactgtg tgcatatctg atccaaaatt aagttttgat gcaatgacga tcgttggaaa
      961 tctcaaccga gacaacgctc aagccctttc taaatttatg agtgtagagc cccaaataag
     1021 actttgggat attcttcaaa caaagtttaa agctaaagca cttcaagaaa aagtttatat
     1081 tgaatatgac aaagtgaaag cagatagttg ggatagacgt aatatgcgta ttgaatttaa
     1141 tccaaacaaa cttacacgag atgaaatgat ttggttaaaa caaaatataa taagctacat
     1201 ggaagatgac ggttttacaa gattagattt agcctttgat tttgaagatg atttgagtga
     1261 ctactatgca atgtctgata aagcagttaa gaaaactatt ttttatggtc gtaatggtaa
     1321 gccagaaaca aaatattttg gcgtgagaga tagtaataga tttattagaa tttataataa
     1381 aaagcaagaa cgtaaagata atgcagatgc tgaagttatg tctgaacatt tatggcgtgt
     1441 agaaatcgaa cttaaaagag atatggtgga ttactggaat gattgcttta gtgatttaca
     1501 tatcttgcaa ccagattgga aaactatcca acgcactgcg gatagagcaa tagtttttat
     1561 gttattgagt gatgaagaag aatggggaaa gcttcacaga aattctagaa caaaatataa
     1621 gaatttgata aaagaaattt cgccagtcga tttaacggac ttaatgaaat cgactttaaa
     1681 agcgaacgaa aaacaattgc aaaaacaaat cgatttttgg caacatgaat ttaaattttg
     1741 gaaatagtgt acatattaat attactgaac aaaaatgata tatttaaact attctaattt
     1801 aggaggattt ttttatgaag tgtctattta aaaatttggg gaatttatat gaggtgaaag
     1861 aataatttac ccctataaac tttagtcacc tcaagtaaag aggtaaaatt gtttagttta
     1921 tataaaaaat ttaaaggttt gttttatagc gttttatttt ggctttgtat tctttcattt
     1981 tttagtgtat taaatgaaat ggttttaaat gtttctttac ctgatattgc aaatcatttt
     2041 aatactactc ctggaattac aaactgggta aacactgcat atatgttaac tttttcgata
     2101 ggaacagcag tatatggaaa attatctgat tatataaata taaaaaaatt gttaattatt
     2161 ggtattagtt tgagctgtct tggttcattg attgctttta ttggtcacaa tcactttttt
     2221 attttgattt ttggtaggtt agtacaagga gtaggatctg ctgcattccc ttcactgatt
     2281 atggtggttg tagctagaaa tattacaaga aaaaaacaag gcaaagcctt tggttttata
     2341 ggatcaattg tagctttagg tgaagggtta ggtccttcaa tagggggaat aatagcacat
     2401 tatattcatt ggtcttacct acttatactt cctatgatta caatagtaac tatacctttt
     2461 cttattaaag taatggtacc tggtaaatca acaaaaaata cattagatat cgtaggtatt
     2521 gttttaatgt ctataagtat tatatgtttt atgttattta cgacaaatta taattggact
     2581 tttttaatac tcttcacaat cttttttgtg atttttatta aacatatttc aagagtttct
     2641 aaccctttta ttaatcctaa actagggaaa aacattccgt ttatgcttgg tttgttttct
     2701 ggtgggctaa tattttctat agtagctggt tttatatcaa tggtgcctta tatgatgaaa
     2761 actatttatc atgtaaatgt agcgacaata ggtaatagtg ttatttttcc tggaaccatg
     2821 agtgttattg tttttggtta ttttggtggt tttttagtgg atagaaaagg atcattattt
     2881 gtttttattt taggatcatt gtctatctct ataagttttt taactattgc attttttgtt
     2941 gagtttagta tgtggttgac tacttttatg tttatatttg ttatgggcgg attatctttt
     3001 actaaaacag ttatatcaaa aatagtatca agtagtcttt ctgaagaaga agttgcttct
     3061 ggaatgagtt tgctaaattt cacaagtttt ttatcagagg gaacaggtat agcaattgta
     3121 ggaggtttat tgtcactaca attgattaat cgtaaactag ttctggaatt tataaattat
     3181 tcttctggag tgtatagtaa tattcttgta gccatggcta tccttattat tttatgttgt
     3241 cttttgacga ttattgtatt taaacgttct gaaaagcagt ttgaatagtt atattatatt
     3301 ttggtttaga actatgagtg gctagcattt tgccactcat tttttgcgtt agcaaaaaca
     3361 ggtttaagcc tcgcagagca cacgtattaa cgacttatta aaaataagtc tagtgtgtta
     3421 gacttaaact attaaataca catgaaacct ttgtgcttag gagtgatttt tatatgtctt
     3481 attccattgt tagagtttca aaagttaaat ctggaacaaa tacaacgggc atacaaaaac
     3541 atgttcaaag agaaaataat aattatgaaa atgaagatat agaccatagt aaaacttact
     3601 taaattatga tttggtaaat gctaataaac agaattttaa taacttgatt gatgaaaaaa
     3661 tcgaacagaa ttatacaggc aaaagaaaaa ttagaacaga cgcgattaaa cacattgatg
     3721 gtttaattac atcagacaat gatttctttg ataatcaaac gccagaagat acaaagcagt
     3781 tttttgaata tgctaaagag tttttagaac aagaatacgg taaagataat ttattatatg
     3841 caacagttca catggacgaa aaaacaccac atatgcatta tggcgttgtt ccaataactg
     3901 atgatggtcg tttaagtgct aaagaagttg taggtaataa aaaagcttta acagcgtttc
     3961 aagatagatt taatgagcat gttaaacaac gaggatatga tttagaacgt gggcaatcaa
     4021 gacaagtaac aaatgctaaa catgagcaaa taagtcagta taaacaaaaa acagaatatc
     4081 ataagcaaga atatgaacgt gagagccaaa aaacagacca tataaagcaa aagaacgata
     4141 aattaatgca agagtaccaa aaatcgttaa atacgcttaa aaagcctata aatgttccgt
     4201 atgagcaaga aactgaaaaa gtaggtggtt tatttagcaa agaaatacaa gaaactggaa
     4261 atgttgtaat aagccaaaaa gatttcaatg aatttcagaa acagataaaa gctgctcaag
     4321 atatttcgga agattacgag tatataaagt ctggtagagc cttagatgat aaagataagg
     4381 aaatacgaga gaaagatgat ttattaaata aagcagttga gcgtattgaa aacgcagac
//
