LOCUS       NZ_CP119551             2683 bp    DNA     circular CON 11-APR-2024
DEFINITION  Providencia stuartii strain CAVP490 plasmid pCAVP490-2683, complete
            sequence.
ACCESSION   NZ_CP119551
VERSION     NZ_CP119551.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN33687285
            Assembly: GCF_029277985.1
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  JOURNAL   Unpublished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_029277985.1-RS_2024_03_11
            Annotation Date                   :: 03/11/2024 12:53:50
            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)                     :: 4,279
            CDSs (total)                      :: 4,172
            Genes (coding)                    :: 4,092
            CDSs (with protein)               :: 4,092
            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)              :: 80
            CDSs (without protein)            :: 80
            Pseudo Genes (ambiguous residues) :: 0 of 80
            Pseudo Genes (frameshifted)       :: 33 of 80
            Pseudo Genes (incomplete)         :: 57 of 80
            Pseudo Genes (internal stop)      :: 17 of 80
            Pseudo Genes (multiple problems)  :: 19 of 80
            CRISPR Arrays                     :: 3
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP119551.1.
            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="CAVP490"
                     /isolation_source="human"
                     /host="Homo sapiens"
                     /db_xref="taxon:588"
                     /plasmid="pCAVP490-2683"
                     /geo_loc_name="USA: Virginia"
                     /collected_by="University of Virginia Health System"
     gene            complement(join(2388..2683,1..145))
                     /locus_tag="P2E05_RS21385"
                     /old_locus_tag="P2E05_21385"
     CDS             complement(join(2388..2683,1..145))
                     /locus_tag="P2E05_RS21385"
                     /old_locus_tag="P2E05_21385"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001330917.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_015063446.1"
                     /translation="MSQLFRLASPEDYEYIEELNLWELSFDKRPVQGVRCEDPVIGAEK
                     YNQGREKFKALASRHKKHWKPNGLTFSELIRWAIECGTPEQCQLVLALYHCTNDDDYQA
                     MGIQLSRSIDNANVSPIIFFTGKNQRLLGDISMLKQLEEKVR"
                     /name="hypothetical protein"
     gene            complement(783..1427)
                     /locus_tag="P2E05_RS21390"
                     /old_locus_tag="P2E05_21390"
     CDS             complement(783..1427)
                     /locus_tag="P2E05_RS21390"
                     /old_locus_tag="P2E05_21390"
                     /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             complement(787..1427)
                     /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(1522..1677)
                     /name="Col3M"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="98.089"
                     /coverage="100.0"
                     /evalue="2.29e-71"
ORIGIN
        1 cttgattata tttttctgcc ccgatcaccg gatcttcaca acgaacccct tgaaccggtc
       61 gcttatcaaa tgacaattcc cataaattta attcttcgat gtattcgtaa tcttctggcg
      121 atgccaaacg aaataattga gacatagaga caccctccga tcatgtgtga acggagacag
      181 tataaggctt tcgagaaatt ccgcttcctc gacgtgaaac aagttcacgc cttgcggcga
      241 gcgttgcgaa ttgaatttat gaggtttacc aagctccaga tgtaacaaag ccccgtgaca
      301 gcatcacagg gctctggtac tctaaatctt gtgcattcgt tgctcagatt agacgtcgca
      361 atccaatctt agcaacgtga gaggcgcttg tcacgttctc attaaatacc agccaacgac
      421 attaacccaa atgcaccact tgattgactc ggacttagcc cggtctccga aaggataaac
      481 aggcaaattg tggtagtaaa acgtaccgga aaacgaaatt ccggctctac ctccgaatca
      541 cgctgcggta tcgaaagatt acagtgcgta cctgataaga gcaccaatca acggactagg
      601 gatttcttgg attgcgaagt gtcgaaagaa gcccaaccta accaaactta gccagattaa
      661 cgagctaaga gaccatgacc caataactga tcatggagaa aagcaaagac aagatgaaga
      721 tgtcgcttcg ctccgttttg attagtacca cattggggca ttaggcgttt tttacctaga
      781 ttttatcggt gaacaataac acctaaactc tcaacaagct gaagcgcctg ctctccatcc
      841 aacttcactc catctaaatt aattcgcctt gcatcaagct cgccaagcgc cccacccgtt
      901 aaatcacaac cagtaaaatc agccaaagac caatcaaacg atgaaaactc cccacaagaa
      961 agatcggagc cacgaaacac ggcgccagtt atcacagtgc cattccagcg attttcccac
     1021 agttcgcact tttctaatat gactctagaa aaattagcgt aactaagatt tgtcttggtt
     1081 atataagcac tacaaaacca tgaccttgta gttatcatat tcataaaatt agcccctcga
     1141 aaatcagctc cttgagctaa acactcacta atttcaagac ctaaggcgct aatgttttta
     1201 aaattactca ttgataaatc gcagctttta aagctagcgt tttttagttt ggctctatta
     1261 aaatcacacc cttccaagct attcctgtcg taaaaactac aatcaacaaa ttcagtatca
     1321 gttaaatcaa cccctgaaaa atcacaattt gaaaaggcaa tatttttaac tctattcccc
     1381 gtaaattgat ctcgtgaaaa cttttcattg ataaagtgct tttccataca tgctacacct
     1441 ggttatttat acagtgcaat cattgtacat taatttgaac aaccttaaac tctagctaaa
     1501 attgattcat acaatccctt ttatgttaaa cgggcgagtt agttagcaaa aacctcccgt
     1561 tcatccccat taaagcccct cgaaacgatt ttaagacacg atcaccctat aaaacaccca
     1621 aatctacgct gaaagtttag aacggttttg cgggcttctg agtgcgtttt taacatcgtg
     1681 caaactgaca agtaaaacga tgcgaaatcg ctgaaagtca caaacttgtt ttgtggcaag
     1741 aagcgatttg accaaccgag taaaacgagg gcggtaggct ttttgttttt atcctgatga
     1801 gcgtccagcg aagaaaggga aaaacagggg gagccgaaac gaaatgacac gccccagcga
     1861 tggcaagtga accccagtga acgtgtttcg ttttgggggc aaagcccccc gtcaagcgaa
     1921 gcgtctgacc accacatttt tgagcgacca aatacagggg cgaaaaaagg gggtggtcag
     1981 acgaacgcag tgagtttgac gggcttgggt gaatggtttt tttcgcaggc gtccagccga
     2041 agaaaatagc cagagggcgg agccttatgt cattcatttt cgtccagaaa atgagtggca
     2101 ttgatactga aagtatcatg gggtgcaagt tagtaaaact atgattctac ccattatttc
     2161 acccgttatt ctgcccgtta tacctaaatt gggtgcaata acgggtaaag taataggtag
     2221 aataacaggt ggattaatgg gtaagaaata acacaacgtc atcttgtgtc tatctattat
     2281 tctgtatctt attctatgta ttattctacc tattacagac gaaatagata aaataagaga
     2341 tagaataata gataggataa tacataaaat aataggtaaa cctaacgtca gcgcaccttt
     2401 tcttcgagct gttttagcat cgaaatatca cctaataacc gttgattttt acctgtgaaa
     2461 aagatgatcg gactgacatt tgcattatca atacttcggc ttaactgaat tcccatcgcc
     2521 tgataatcat catcgtttgt gcaatggtat aacgctaaaa caagctgaca ttgttctgga
     2581 gttccgcatt ctattgccca gcggatcaac tccgaaaagg tcaatccgtt cggtttccag
     2641 tgttttttat gccgtgacgc taacgcctta aatttttcac gcc
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