LOCUS       NZ_CP119545             2683 bp    DNA     circular CON 11-MAR-2024
DEFINITION  Providencia stuartii strain CAVP496 plasmid pCAVP496-2683, complete
            sequence.
ACCESSION   NZ_CP119545
VERSION     NZ_CP119545.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN33687286
            Assembly: GCF_029277825.1
KEYWORDS    RefSeq.
SOURCE      Providencia stuartii
  ORGANISM  Providencia stuartii
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Morganellaceae; Providencia.
REFERENCE   1  (bases 1 to 2683)
  AUTHORS   Patel,A., Salomon,M., Barry,K., Parikh,H.I., Elliot,Z.S.,
            Fleece,M.E. and Mathers,A.J.
  TITLE     Management of PER-1 and NDM-producing Providencia stuartii
            bacteremia in a patient with a severe beta-lactam allergy: the
            increasing need for aztreonam-avibactam
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 2683)
  AUTHORS   Patel,A., Salomon,M., Barry,K., Parikh,H.I., Elliot,Z.S.,
            Fleece,M.E. and Mathers,A.J.
  TITLE     Direct Submission
  JOURNAL   Submitted (08-MAR-2023) School of Medicine, University of Virginia,
            409 Lane Road, Charlottesville, VA 22908, USA
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: Unicycler v. v0.5.0
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 100X
            Sequencing Technology :: Illumina MiSeq + Oxford Nanopore MinION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_029277825.1-RS_2024_03_11
            Annotation Date                   :: 03/11/2024 12:51:51
            Annotation Pipeline :: NCBI Prokaryotic Genome Annotation Pipeline
            (PGAP)
            Annotation Method :: Best-placed reference protein set; GeneMarkS-2+
            Annotation Software revision      :: 6.7
            Features Annotated                :: Gene; CDS; rRNA; tRNA; ncRNA
            Genes (total)                     :: 4,307
            CDSs (total)                      :: 4,201
            Genes (coding)                    :: 4,118
            CDSs (with protein)               :: 4,118
            Genes (RNA)                       :: 106
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 77
            ncRNAs                            :: 7
            Pseudo Genes (total)              :: 83
            CDSs (without protein)            :: 83
            Pseudo Genes (ambiguous residues) :: 0 of 83
            Pseudo Genes (frameshifted)       :: 33 of 83
            Pseudo Genes (incomplete)         :: 59 of 83
            Pseudo Genes (internal stop)      :: 18 of 83
            Pseudo Genes (multiple problems)  :: 19 of 83
            CRISPR Arrays                     :: 3
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP119545.1.
            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..2683
                     /organism="Providencia stuartii"
                     /mol_type="genomic DNA"
                     /strain="CAVP496"
                     /isolation_source="human"
                     /host="Homo sapiens"
                     /db_xref="taxon:588"
                     /plasmid="pCAVP496-2683"
                     /geo_loc_name="USA: Virginia"
                     /collected_by="University of Virginia Health System"
     gene            complement(366..1010)
                     /locus_tag="P2E04_RS21525"
                     /old_locus_tag="P2E04_21525"
     CDS             complement(366..1010)
                     /locus_tag="P2E04_RS21525"
                     /old_locus_tag="P2E04_21525"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_032495680.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="quinolone resistance pentapeptide repeat protein
                     QnrD1"
                     /protein_id="WP_012634451.1"
                     /translation="MEKHFINEKFSRDQFTGNRVKNIAFSNCDFSGVDLTDTEFVDCSF
                     YDRNSLEGCDFNRAKLKNASFKSCDLSMSNFKNISALGLEISECLAQGADFRGANFMNM
                     ITTRSWFCSAYITKTNLSYANFSRVILEKCELWENRWNGTVITGAVFRGSDLSCGEFSS
                     FDWSLADFTGCDLTGGALGELDARRINLDGVKLDGEQALQLVESLGVIVHR"
                     /name="quinolone resistance pentapeptide repeat protein
                     QnrD1"
     gene            complement(1971..2411)
                     /locus_tag="P2E04_RS21530"
                     /old_locus_tag="P2E04_21530"
     CDS             complement(1971..2411)
                     /locus_tag="P2E04_RS21530"
                     /old_locus_tag="P2E04_21530"
                     /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_015063446.1"
                     /translation="MSQLFRLASPEDYEYIEELNLWELSFDKRPVQGVRCEDPVIGAEK
                     YNQGREKFKALASRHKKHWKPNGLTFSELIRWAIECGTPEQCQLVLALYHCTNDDDYQA
                     MGIQLSRSIDNANVSPIIFFTGKNQRLLGDISMLKQLEEKVR"
                     /name="hypothetical protein"
     ARG             complement(370..1010)
                     /name="qnrD1"
                     /gene="qnrD1"
                     /gene_name="quinolone resistance pentapeptide repeat
                     protein QnrD1"
                     /tool="amrfinderplus"
                     /drug_class="QUINOLONE"
                     /identity="100.0"
                     /coverage="100.0"
     Typing          complement(1105..1260)
                     /name="Col3M"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="98.089"
                     /coverage="100.0"
                     /evalue="2.29e-71"
ORIGIN
        1 gacattaacc caaatgcacc acttgattga ctcggactta gcccggtctc cgaaaggata
       61 aacaggcaaa ttgtggtagt aaaacgtacc ggaaaacgaa attccggctc tacctccgaa
      121 tcacgctgcg gtatcgaaag attacagtgc gtacctgata agagcaccaa tcaacggact
      181 agggatttct tggattgcga agtgtcgaaa gaagcccaac ctaaccaaac ttagccagat
      241 taacgagcta agagaccatg acccaataac tgatcatgga gaaaagcaaa gacaagatga
      301 agatgtcgct tcgctccgtt ttgattagta ccacattggg gcattaggcg ttttttacct
      361 agattttatc ggtgaacaat aacacctaaa ctctcaacaa gctgaagcgc ctgctctcca
      421 tccaacttca ctccatctaa attaattcgc cttgcatcaa gctcgccaag cgccccaccc
      481 gttaaatcac aaccagtaaa atcagccaaa gaccaatcaa acgatgaaaa ctccccacaa
      541 gaaagatcgg agccacgaaa cacggcgcca gttatcacag tgccattcca gcgattttcc
      601 cacagttcgc acttttctaa tatgactcta gaaaaattag cgtaactaag atttgtcttg
      661 gttatataag cactacaaaa ccatgacctt gtagttatca tattcataaa attagcccct
      721 cgaaaatcag ctccttgagc taaacactca ctaatttcaa gacctaaggc gctaatgttt
      781 ttaaaattac tcattgataa atcgcagctt ttaaagctag cgttttttag tttggctcta
      841 ttaaaatcac acccttccaa gctattcctg tcgtaaaaac tacaatcaac aaattcagta
      901 tcagttaaat caacccctga aaaatcacaa tttgaaaagg caatattttt aactctattc
      961 cccgtaaatt gatctcgtga aaacttttca ttgataaagt gcttttccat acatgctaca
     1021 cctggttatt tatacagtgc aatcattgta cattaatttg aacaacctta aactctagct
     1081 aaaattgatt catacaatcc cttttatgtt aaacgggcga gttagttagc aaaaacctcc
     1141 cgttcatccc cattaaagcc cctcgaaacg attttaagac acgatcaccc tataaaacac
     1201 ccaaatctac gctgaaagtt tagaacggtt ttgcgggctt ctgagtgcgt ttttaacatc
     1261 gtgcaaactg acaagtaaaa cgatgcgaaa tcgctgaaag tcacaaactt gttttgtggc
     1321 aagaagcgat ttgaccaacc gagtaaaacg agggcggtag gctttttgtt tttatcctga
     1381 tgagcgtcca gcgaagaaag ggaaaaacag ggggagccga aacgaaatga cacgccccag
     1441 cgatggcaag tgaaccccag tgaacgtgtt tcgttttggg ggcaaagccc cccgtcaagc
     1501 gaagcgtctg accaccacat ttttgagcga ccaaatacag gggcgaaaaa agggggtggt
     1561 cagacgaacg cagtgagttt gacgggcttg ggtgaatggt ttttttcgca ggcgtccagc
     1621 cgaagaaaat agccagaggg cggagcctta tgtcattcat tttcgtccag aaaatgagtg
     1681 gcattgatac tgaaagtatc atggggtgca agttagtaaa actatgattc tacccattat
     1741 ttcacccgtt attctgcccg ttatacctaa attgggtgca ataacgggta aagtaatagg
     1801 tagaataaca ggtggattaa tgggtaagaa ataacacaac gtcatcttgt gtctatctat
     1861 tattctgtat cttattctat gtattattct acctattaca gacgaaatag ataaaataag
     1921 agatagaata atagatagga taatacataa aataataggt aaacctaacg tcagcgcacc
     1981 ttttcttcga gctgttttag catcgaaata tcacctaata accgttgatt tttacctgtg
     2041 aaaaagatga tcggactgac atttgcatta tcaatacttc ggcttaactg aattcccatc
     2101 gcctgataat catcatcgtt tgtgcaatgg tataacgcta aaacaagctg acattgttct
     2161 ggagttccgc attctattgc ccagcggatc aactccgaaa aggtcaatcc gttcggtttc
     2221 cagtgttttt tatgccgtga cgctaacgcc ttaaattttt cacgcccttg attatatttt
     2281 tctgccccga tcaccggatc ttcacaacga accccttgaa ccggtcgctt atcaaatgac
     2341 aattcccata aatttaattc ttcgatgtat tcgtaatctt ctggcgatgc caaacgaaat
     2401 aattgagaca tagagacacc ctccgatcat gtgtgaacgg agacagtata aggctttcga
     2461 gaaattccgc ttcctcgacg tgaaacaagt tcacgccttg cggcgagcgt tgcgaattga
     2521 atttatgagg tttaccaagc tccagatgta acaaagcccc gtgacagcat cacagggctc
     2581 tggtactcta aatcttgtgc attcgttgct cagattagac gtcgcaatcc aatcttagca
     2641 acgtgagagg cgcttgtcac gttctcatta aataccagcc aac
//
