LOCUS       NZ_CP132558             4439 bp    DNA     circular CON 24-AUG-2023
DEFINITION  Staphylococcus saprophyticus strain SZ.PL35w plasmid pSZ.PL35w,
            complete sequence.
ACCESSION   NZ_CP132558
VERSION     NZ_CP132558.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN36970803
            Assembly: GCF_030845315.1
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 PL35w, 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  JOURNAL   Unpublished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_PL35w_Novo04_10_49Flow_8_S_sap
            rophyticus
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 231.0x
            Sequencing Technology :: Illumina NovaSeq; Oxford Nanopore MinION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 08/21/2023 16:33:18
            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
            CP132558.1.
            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.PL35w"
                     /isolation_source="fingertip"
                     /host="Homo sapiens"
                     /db_xref="taxon:29385"
                     /plasmid="pSZ.PL35w"
                     /geo_loc_name="Hong Kong: Telegraph Bay"
                     /lat_lon="22.2642601 N 114.1299767 E"
                     /collection_date="2022-11-22"
                     /collected_by="Sarah S. Q. Zhang"
     gene            join(3094..4439,1..34)
                     /gene="tet(K)"
                     /locus_tag="RA083_RS12895"
                     /old_locus_tag="RA083_12890"
     ARG             3095..4437
                     /name="tet(K)"
                     /gene="tet(K)"
                     /gene_name="tetracycline efflux MFS transporter Tet(K)"
                     /tool="amrfinderplus"
                     /drug_class="TETRACYCLINE"
                     /identity="100.0"
                     /coverage="97.6"
     gene            220..1461
                     /gene="mobV"
                     /locus_tag="RA083_RS12900"
                     /old_locus_tag="RA083_12895"
     CDS             220..1461
                     /gene="mobV"
                     /locus_tag="RA083_RS12900"
                     /old_locus_tag="RA083_12895"
                     /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            1988..2932
                     /locus_tag="RA083_RS12905"
                     /old_locus_tag="RA083_12900"
     CDS             1988..2932
                     /locus_tag="RA083_RS12905"
                     /old_locus_tag="RA083_12900"
                     /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"
     Typing          1989..2932
                     /name="rep_cluster_1118"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          221..1458
                     /name="MOBV"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 tgtatttaaa cgttctgaaa agcagtttga atagttatat tatattttgg tttagaacta
       61 tgagtggcta gcattttgcc actcattttt tgcgttagca aaaacaggtt taagcctcgc
      121 agagcacacg tattaacgac ttattaaaaa taagtctagt gtgttagact taaactatta
      181 aatacacatg aaacctttgt gcttaggagt gatttttata tgtcttattc cattgttaga
      241 gtttcaaaag ttaaatctgg aacaaataca acgggcatac aaaaacatgt tcaaagagaa
      301 aataataatt atgaaaatga agatatagac catagtaaaa cttacttaaa ttatgatttg
      361 gtaaatgcta ataaacagaa ttttaataac ttgattgatg aaaaaatcga acagaattat
      421 acaggcaaaa gaaaaattag aacagacgcg attaaacaca ttgatggttt aattacatca
      481 gacaatgatt tctttgataa tcaaacgcca gaagatacaa agcagttttt tgaatatgct
      541 aaagagtttt tagaacaaga atacggtaaa gataatttat tatatgcaac agttcacatg
      601 gacgaaaaaa caccacatat gcattatggc gttgttccaa taactgatga tggtcgttta
      661 agtgctaaag aagttgtagg taataaaaaa gctttaacag cgtttcaaga tagatttaat
      721 gagcatgtta aacaacgagg atatgattta gaacgtgggc aatcaagaca agtaacaaat
      781 gctaaacatg agcaaataag tcagtataaa caaaaaacag aatatcataa gcaagaatat
      841 gaacgtgaga gccaaaaaac agaccatata aagcaaaaga acgataaatt aatgcaagag
      901 taccaaaaat cgttaaatac gcttaaaaag cctataaatg ttccgtatga gcaagaaact
      961 gaaaaagtag gtggtttatt tagcaaagaa atacaagaaa ctggaaatgt tgtaataagc
     1021 caaaaagatt tcaatgaatt tcagaaacag ataaaagctg ctcaagatat ttcggaagat
     1081 tacgagtata taaagtctgg tagagcctta gatgataaag ataaggaaat acgagagaaa
     1141 gatgatttat taaataaagc agttgagcgt attgaaaacg cagacgataa ttttaaccaa
     1201 ctttacgaaa atgcaaagcc acttaaagag aatatagaaa tagcgttaaa gcttttaaaa
     1261 atcttactaa aagagttaga acgagtttta ggaagaaata cctttgcgga aagagttaat
     1321 aagttaacag aagatgaacc aaaactaaat ggtttagcag gaaacttaga taaaaaaatg
     1381 aatccagaat tatattcaga acaggaacag caacaagaac aacaaaagaa tcaaaaacga
     1441 gatagaggta tgcacttata gaacatgcat ttatgccgag aaaacttatt ggttggaatg
     1501 ggctatgtgt tagctaactt gttagcgagt tggttggact tgaattggga ttaatcccaa
     1561 gaaagtacca actcaacaac acataaagcc ctgtaggttc cgaccaataa ggaaattgga
     1621 ataaagcaat aaaaggagtt gaagaaatga aattcagaga agcctttgag aattttataa
     1681 caagtaagta tgtacttggt gttttagtag ttttaactgt ttaccagata atacaaatgc
     1741 ttaaataaaa aaagacttga tctgattaga ccaagtcttt tgatagtgtt atattaataa
     1801 caaaataaaa aggagtcgct cacgccctga ccaaagtttg tgaacgacat cattcaaaga
     1861 aaaaaacact gagttgtttt tataatcttg tatatttaga tattaaacga tatttaaata
     1921 tacatcaaga tatatatttg ggtgagcgat tccttaaacg aaattgagat taaggagtcg
     1981 attttttatg tataaaaaca atcatgcaaa tcattcaaat catttggaaa atcacgattt
     2041 agacaatttt tctaaaaccg gctactctaa tagccggttg gacgcacata ctgtgtgcat
     2101 atctgatcca aaattaagtt ttgatgcaat gacgatcgtt ggaaatctca accgagacaa
     2161 cgctcaagcc ctttctaaat ttatgagtgt agagccccaa ataagacttt gggatattct
     2221 tcaaacaaag tttaaagcta aagcacttca agaaaaagtt tatattgaat atgacaaagt
     2281 gaaagcagat agttgggata gacgtaatat gcgtattgaa tttaatccaa acaaacttac
     2341 acgagatgaa atgatttggt taaaacaaaa tataataagc tacatggaag atgacggttt
     2401 tacaagatta gatttagcct ttgattttga agatgatttg agtgactact atgcaatgtc
     2461 tgataaagca gttaagaaaa ctatttttta tggtcgtaat ggtaagccag aaacaaaata
     2521 ttttggcgtg agagatagta atagatttat tagaatttat aataaaaagc aagaacgtaa
     2581 agataatgca gatgctgaag ttatgtctga acatttatgg cgtgtagaaa tcgaacttaa
     2641 aagagatatg gtggattact ggaatgattg ctttagtgat ttacatatct tgcaaccaga
     2701 ttggaaaact atccaacgca ctgcggatag agcaatagtt tttatgttat tgagtgatga
     2761 agaagaatgg ggaaagcttc acagaaattc tagaacaaaa tataagaatt tgataaaaga
     2821 aatttcgcca gtcgatttaa cggacttaat gaaatcgact ttaaaagcga acgaaaaaca
     2881 attgcaaaaa caaatcgatt tttggcaaca tgaatttaaa ttttggaaat agtgtacata
     2941 ttaatattac tgaacaaaaa tgatatattt aaactattct aatttaggag gattttttta
     3001 tgaagtgtct atttaaaaat ttggggaatt tatatgaggt gaaagaataa tttaccccta
     3061 taaactttag tcacctcaag taaagaggta aaattgttta gtttatataa aaaatttaaa
     3121 ggtttgtttt atagcgtttt attttggctt tgtattcttt cattttttag tgtattaaat
     3181 gaaatggttt taaatgtttc tttacctgat attgcaaatc attttaatac tactcctgga
     3241 attacaaact gggtaaacac tgcatatatg ttaacttttt cgataggaac agcagtatat
     3301 ggaaaattat ctgattatat aaatataaaa aaattgttaa ttattggtat tagtttgagc
     3361 tgtcttggtt cattgattgc ttttattggt cacaatcact tttttatttt gatttttggt
     3421 aggttagtac aaggagtagg atctgctgca ttcccttcac tgattatggt ggttgtagct
     3481 agaaatatta caagaaaaaa acaaggcaaa gcctttggtt ttataggatc aattgtagct
     3541 ttaggtgaag ggttaggtcc ttcaataggg ggaataatag cacattatat tcattggtct
     3601 tacctactta tacttcctat gattacaata gtaactatac cttttcttat taaagtaatg
     3661 gtacctggta aatcaacaaa aaatacatta gatatcgtag gtattgtttt aatgtctata
     3721 agtattatat gttttatgtt atttacgaca aattataatt ggactttttt aatactcttc
     3781 acaatctttt ttgtgatttt tattaaacat atttcaagag tttctaaccc ttttattaat
     3841 cctaaactag ggaaaaacat tccgtttatg cttggtttgt tttctggtgg gctaatattt
     3901 tctatagtag ctggttttat atcaatggtg ccttatatga tgaaaactat ttatcatgta
     3961 aatgtagcga caataggtaa tagtgttatt tttcctggaa ccatgagtgt tattgttttt
     4021 ggttattttg gtggtttttt agtggataga aaaggatcat tatttgtttt tattttagga
     4081 tcattgtcta tctctataag ttttttaact attgcatttt ttgttgagtt tagtatgtgg
     4141 ttgactactt ttatgtttat atttgttatg ggcggattat cttttactaa aacagttata
     4201 tcaaaaatag tatcaagtag tctttctgaa gaagaagttg cttctggaat gagtttgcta
     4261 aatttcacaa gttttttatc agagggaaca ggtatagcaa ttgtaggagg tttattgtca
     4321 ctacaattga ttaatcgtaa actagttctg gaatttataa attattcttc tggagtgtat
     4381 agtaatattc ttgtagccat ggctatcctt attattttat gttgtctttt gacgattat
//
