LOCUS       NZ_CP119558             2683 bp    DNA     circular CON 11-MAR-2024
DEFINITION  Providencia stuartii strain CAVP450 plasmid pCAVP450-2683, complete
            sequence.
ACCESSION   NZ_CP119558
VERSION     NZ_CP119558.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN33687284
            Assembly: GCF_029278185.1
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  JOURNAL   Unpublished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_029278185.1-RS_2024_03_11
            Annotation Date                   :: 03/11/2024 12:51:16
            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)                     :: 4,311
            CDSs (total)                      :: 4,204
            Genes (coding)                    :: 4,121
            CDSs (with protein)               :: 4,121
            Genes (RNA)                       :: 107
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 78
            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)         :: 60 of 83
            Pseudo Genes (internal stop)      :: 17 of 83
            Pseudo Genes (multiple problems)  :: 19 of 83
            CRISPR Arrays                     :: 3
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP119558.1.
            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="CAVP450"
                     /isolation_source="human"
                     /host="Homo sapiens"
                     /db_xref="taxon:588"
                     /plasmid="pCAVP450-2683"
                     /geo_loc_name="USA: Virginia"
                     /collected_by="University of Virginia Health System"
     gene            121..561
                     /locus_tag="P2E06_RS21545"
                     /old_locus_tag="P2E06_21545"
     CDS             121..561
                     /locus_tag="P2E06_RS21545"
                     /old_locus_tag="P2E06_21545"
                     /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"
     gene            1522..2166
                     /locus_tag="P2E06_RS21550"
                     /old_locus_tag="P2E06_21550"
     CDS             1522..2166
                     /locus_tag="P2E06_RS21550"
                     /old_locus_tag="P2E06_21550"
                     /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"
     ARG             1523..2163
                     /name="qnrD1"
                     /gene="qnrD1"
                     /gene_name="quinolone resistance pentapeptide repeat
                     protein QnrD1"
                     /tool="amrfinderplus"
                     /drug_class="QUINOLONE"
                     /identity="100.0"
                     /coverage="100.0"
     Typing          1273..1428
                     /name="Col3M"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="98.089"
                     /coverage="100.0"
                     /evalue="2.29e-71"
ORIGIN
        1 acctcataaa ttcaattcgc aacgctcgcc gcaaggcgtg aacttgtttc acgtcgagga
       61 agcggaattt ctcgaaagcc ttatactgtc tccgttcaca catgatcgga gggtgtctct
      121 atgtctcaat tatttcgttt ggcatcgcca gaagattacg aatacatcga agaattaaat
      181 ttatgggaat tgtcatttga taagcgaccg gttcaagggg ttcgttgtga agatccggtg
      241 atcggggcag aaaaatataa tcaagggcgt gaaaaattta aggcgttagc gtcacggcat
      301 aaaaaacact ggaaaccgaa cggattgacc ttttcggagt tgatccgctg ggcaatagaa
      361 tgcggaactc cagaacaatg tcagcttgtt ttagcgttat accattgcac aaacgatgat
      421 gattatcagg cgatgggaat tcagttaagc cgaagtattg ataatgcaaa tgtcagtccg
      481 atcatctttt tcacaggtaa aaatcaacgg ttattaggtg atatttcgat gctaaaacag
      541 ctcgaagaaa aggtgcgctg acgttaggtt tacctattat tttatgtatt atcctatcta
      601 ttattctatc tcttatttta tctatttcgt ctgtaatagg tagaataata catagaataa
      661 gatacagaat aatagataga cacaagatga cgttgtgtta tttcttaccc attaatccac
      721 ctgttattct acctattact ttacccgtta ttgcacccaa tttaggtata acgggcagaa
      781 taacgggtga aataatgggt agaatcatag ttttactaac ttgcacccca tgatactttc
      841 agtatcaatg ccactcattt tctggacgaa aatgaatgac ataaggctcc gccctctggc
      901 tattttcttc ggctggacgc ctgcgaaaaa aaccattcac ccaagcccgt caaactcact
      961 gcgttcgtct gaccaccccc ttttttcgcc cctgtatttg gtcgctcaaa aatgtggtgg
     1021 tcagacgctt cgcttgacgg ggggctttgc ccccaaaacg aaacacgttc actggggttc
     1081 acttgccatc gctggggcgt gtcatttcgt ttcggctccc cctgtttttc cctttcttcg
     1141 ctggacgctc atcaggataa aaacaaaaag cctaccgccc tcgttttact cggttggtca
     1201 aatcgcttct tgccacaaaa caagtttgtg actttcagcg atttcgcatc gttttacttg
     1261 tcagtttgca cgatgttaaa aacgcactca gaagcccgca aaaccgttct aaactttcag
     1321 cgtagatttg ggtgttttat agggtgatcg tgtcttaaaa tcgtttcgag gggctttaat
     1381 ggggatgaac gggaggtttt tgctaactaa ctcgcccgtt taacataaaa gggattgtat
     1441 gaatcaattt tagctagagt ttaaggttgt tcaaattaat gtacaatgat tgcactgtat
     1501 aaataaccag gtgtagcatg tatggaaaag cactttatca atgaaaagtt ttcacgagat
     1561 caatttacgg ggaatagagt taaaaatatt gccttttcaa attgtgattt ttcaggggtt
     1621 gatttaactg atactgaatt tgttgattgt agtttttacg acaggaatag cttggaaggg
     1681 tgtgatttta atagagccaa actaaaaaac gctagcttta aaagctgcga tttatcaatg
     1741 agtaatttta aaaacattag cgccttaggt cttgaaatta gtgagtgttt agctcaagga
     1801 gctgattttc gaggggctaa ttttatgaat atgataacta caaggtcatg gttttgtagt
     1861 gcttatataa ccaagacaaa tcttagttac gctaattttt ctagagtcat attagaaaag
     1921 tgcgaactgt gggaaaatcg ctggaatggc actgtgataa ctggcgccgt gtttcgtggc
     1981 tccgatcttt cttgtgggga gttttcatcg tttgattggt ctttggctga ttttactggt
     2041 tgtgatttaa cgggtggggc gcttggcgag cttgatgcaa ggcgaattaa tttagatgga
     2101 gtgaagttgg atggagagca ggcgcttcag cttgttgaga gtttaggtgt tattgttcac
     2161 cgataaaatc taggtaaaaa acgcctaatg ccccaatgtg gtactaatca aaacggagcg
     2221 aagcgacatc ttcatcttgt ctttgctttt ctccatgatc agttattggg tcatggtctc
     2281 ttagctcgtt aatctggcta agtttggtta ggttgggctt ctttcgacac ttcgcaatcc
     2341 aagaaatccc tagtccgttg attggtgctc ttatcaggta cgcactgtaa tctttcgata
     2401 ccgcagcgtg attcggaggt agagccggaa tttcgttttc cggtacgttt tactaccaca
     2461 atttgcctgt ttatcctttc ggagaccggg ctaagtccga gtcaatcaag tggtgcattt
     2521 gggttaatgt cgttggctgg tatttaatga gaacgtgaca agcgcctctc acgttgctaa
     2581 gattggattg cgacgtctaa tctgagcaac gaatgcacaa gatttagagt accagagccc
     2641 tgtgatgctg tcacggggct ttgttacatc tggagcttgg taa
//
