LOCUS       NZ_CP054447             4439 bp    DNA     circular CON 12-SEP-2023
DEFINITION  Staphylococcus saprophyticus strain UTI-056 plasmid pUTI-056-3,
            complete sequence.
ACCESSION   NZ_CP054447
VERSION     NZ_CP054447.1
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 4439)
  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  JOURNAL   Unpublished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 4439)
  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
            CP054447.1.
            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..4439
                     /organism="Staphylococcus saprophyticus"
                     /mol_type="genomic DNA"
                     /strain="UTI-056"
                     /isolation_source="urine specimens"
                     /host="Homo sapiens"
                     /db_xref="taxon:29385"
                     /plasmid="pUTI-056-3"
                     /geo_loc_name="USA: California"
                     /collection_date="2019"
     gene            complement(434..1675)
                     /gene="mobV"
                     /locus_tag="HSZ51_RS13070"
                     /old_locus_tag="HSZ51_13070"
     CDS             complement(434..1675)
                     /gene="mobV"
                     /locus_tag="HSZ51_RS13070"
                     /old_locus_tag="HSZ51_13070"
                     /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            complement(1861..3240)
                     /gene="tet(K)"
                     /locus_tag="HSZ51_RS13075"
                     /old_locus_tag="HSZ51_13075"
     ARG             complement(1865..3240)
                     /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"
     gene            complement(3402..4346)
                     /locus_tag="HSZ51_RS13080"
                     /old_locus_tag="HSZ51_13080"
     CDS             complement(3402..4346)
                     /locus_tag="HSZ51_RS13080"
                     /old_locus_tag="HSZ51_13080"
                     /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          complement(3403..4346)
                     /name="rep_cluster_1118"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          complement(438..1675)
                     /name="MOBV"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 tatacaagat tataaaaaca actcagtgtt tttttctttg aatgatgtcg ttcacaaact
       61 ttggtcaggg cgtgagcgac tcctttttat tttgttatta atataacact atcaaaagac
      121 ttggtctaat cagatcaagt ctttttttat ttaagcattt gtattatctg gtaaacagtt
      181 aaaactacta aaacaccaag tacatactta cttgttataa aattctcaaa ggcttctctg
      241 aatttcattt cttcaactcc ttttattgct ttattccaat ttccttattg gtcggaacct
      301 acagggcttt atgtgttgtt gagttggtac tttcttggga ttaatcccaa ttcaagtcca
      361 accaactcgc taacaagtta gctaacacat agcccattcc aaccaataag ttttctcggc
      421 ataaatgcat gttctataag tgcatacctc tatctcgttt ttgattcttt tgttgttctt
      481 gttgctgttc ctgttctgaa tataattctg gattcatttt tttatctaag tttcctgcta
      541 aaccatttag ttttggttca tcttctgtta acttattaac tctttccgca aaggtatttc
      601 ttcctaaaac tcgttctaac tcttttagta agatttttaa aagctttaac gctatttcta
      661 tattctcttt aagtggcttt gcattttcgt aaagttggtt aaaattatcg tctgcgtttt
      721 caatacgctc aactgcttta tttaataaat catctttctc tcgtatttcc ttatctttat
      781 catctaaggc tctaccagac tttatatact cgtaatcttc cgaaatatct tgagcagctt
      841 ttatctgttt ctgaaattca ttgaaatctt tttggcttat tacaacattt ccagtttctt
      901 gtatttcttt gctaaataaa ccacctactt tttcagtttc ttgctcatac ggaacattta
      961 taggcttttt aagcgtattt aacgattttt ggtactcttg cattaattta tcgttctttt
     1021 gctttatatg gtctgttttt tggctctcac gttcatattc ttgcttatga tattctgttt
     1081 tttgtttata ctgacttatt tgctcatgtt tagcatttgt tacttgtctt gattgcccac
     1141 gttctaaatc atatcctcgt tgtttaacat gctcattaaa tctatcttga aacgctgtta
     1201 aagctttttt attacctaca acttctttag cacttaaacg accatcatca gttattggaa
     1261 caacgccata atgcatatgt ggtgtttttt cgtccatgtg aactgttgca tataataaat
     1321 tatctttacc gtattcttgt tctaaaaact ctttagcata ttcaaaaaac tgctttgtat
     1381 cttctggcgt ttgattatca aagaaatcat tgtctgatgt aattaaacca tcaatgtgtt
     1441 taatcgcgtc tgttctaatt tttcttttgc ctgtataatt ctgttcgatt ttttcatcaa
     1501 tcaagttatt aaaattctgt ttattagcat ttaccaaatc ataatttaag taagttttac
     1561 tatggtctat atcttcattt tcataattat tattttctct ttgaacatgt ttttgtatgc
     1621 ccgttgtatt tgttccagat ttaacttttg aaactctaac aatggaataa gacatataaa
     1681 aatcactcct aagcacaaag gtttcatgtg tatttaatag tttaagtcta acacactaga
     1741 cttattttta ataagtcgtt aatacgtgtg ctctgcgagg cttaaacctg tttttgctaa
     1801 cgcaaaaaat gagtggcaaa atgctagcca ctcatagttc taaaccaaaa tataatataa
     1861 ctattcaaac tgcttttcag aacgtttaaa tacaataatc gtcaaaagac aacataaaat
     1921 aataaggata gccatggcta caagaatatt actatacact ccagaagaat aatttataaa
     1981 ttccagaact agtttacgat taatcaattg tagtgacaat aaacctccta caattgctat
     2041 acctgttccc tctgataaaa aacttgtgaa atttagcaaa ctcattccag aagcaacttc
     2101 ttcttcagaa agactacttg atactatttt tgatataact gttttagtaa aagataatcc
     2161 gcccataaca aatataaaca taaaagtagt caaccacata ctaaactcaa caaaaaatgc
     2221 aatagttaaa aaacttatag agatagacaa tgatcctaaa ataaaaacaa ataatgatcc
     2281 ttttctatcc actaaaaaac caccaaaata accaaaaaca ataacactca tggttccagg
     2341 aaaaataaca ctattaccta ttgtcgctac atttacatga taaatagttt tcatcatata
     2401 aggcaccatt gatataaaac cagctactat agaaaatatt agcccaccag aaaacaaacc
     2461 aagcataaac ggaatgtttt tccctagttt aggattaata aaagggttag aaactcttga
     2521 aatatgttta ataaaaatca caaaaaagat tgtgaagagt attaaaaaag tccaattata
     2581 atttgtcgta aataacataa aacatataat acttatagac attaaaacaa tacctacgat
     2641 atctaatgta ttttttgttg atttaccagg taccattact ttaataagaa aaggtatagt
     2701 tactattgta atcataggaa gtataagtag gtaagaccaa tgaatataat gtgctattat
     2761 tccccctatt gaaggaccta acccttcacc taaagctaca attgatccta taaaaccaaa
     2821 ggctttgcct tgtttttttc ttgtaatatt tctagctaca accaccataa tcagtgaagg
     2881 gaatgcagca gatcctactc cttgtactaa cctaccaaaa atcaaaataa aaaagtgatt
     2941 gtgaccaata aaagcaatca atgaaccaag acagctcaaa ctaataccaa taattaacaa
     3001 tttttttata tttatataat cagataattt tccatatact gctgttccta tcgaaaaagt
     3061 taacatatat gcagtgttta cccagtttgt aattccagga gtagtattaa aatgatttgc
     3121 aatatcaggt aaagaaacat ttaaaaccat ttcatttaat acactaaaaa atgaaagaat
     3181 acaaagccaa aataaaacgc tataaaacaa acctttaaat tttttatata aactaaacaa
     3241 ttttacctct ttacttgagg tgactaaagt ttataggggt aaattattct ttcacctcat
     3301 ataaattccc caaattttta aatagacact tcataaaaaa atcctcctaa attagaatag
     3361 tttaaatata tcatttttgt tcagtaatat taatatgtac actatttcca aaatttaaat
     3421 tcatgttgcc aaaaatcgat ttgtttttgc aattgttttt cgttcgcttt taaagtcgat
     3481 ttcattaagt ccgttaaatc gactggcgaa atttctttta tcaaattctt atattttgtt
     3541 ctagaatttc tgtgaagctt tccccattct tcttcatcac tcaataacat aaaaactatt
     3601 gctctatccg cagtgcgttg gatagttttc caatctggtt gcaagatatg taaatcacta
     3661 aagcaatcat tccagtaatc caccatatct cttttaagtt cgatttctac acgccataaa
     3721 tgttcagaca taacttcagc atctgcatta tctttacgtt cttgcttttt attataaatt
     3781 ctaataaatc tattactatc tctcacgcca aaatattttg tttctggctt accattacga
     3841 ccataaaaaa tagttttctt aactgcttta tcagacattg catagtagtc actcaaatca
     3901 tcttcaaaat caaaggctaa atctaatctt gtaaaaccgt catcttccat gtagcttatt
     3961 atattttgtt ttaaccaaat catttcatct cgtgtaagtt tgtttggatt aaattcaata
     4021 cgcatattac gtctatccca actatctgct ttcactttgt catattcaat ataaactttt
     4081 tcttgaagtg ctttagcttt aaactttgtt tgaagaatat cccaaagtct tatttggggc
     4141 tctacactca taaatttaga aagggcttga gcgttgtctc ggttgagatt tccaacgatc
     4201 gtcattgcat caaaacttaa ttttggatca gatatgcaca cagtatgtgc gtccaaccgg
     4261 ctattagagt agccggtttt agaaaaattg tctaaatcgt gattttccaa atgatttgaa
     4321 tgatttgcat gattgttttt atacataaaa aatcgactcc ttaatctcaa tttcgtttaa
     4381 ggaatcgctc acccaaatat atatcttgat gtatatttaa atatcgttta atatctaaa
//
