LOCUS       NZ_CP119544             3123 bp    DNA     circular CON 11-MAR-2024
DEFINITION  Providencia stuartii strain CAVP496 plasmid pCAVP496-3123, complete
            sequence.
ACCESSION   NZ_CP119544
VERSION     NZ_CP119544.1
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 3123)
  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  JOURNAL   Unpublished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 3123)
  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
            CP119544.1.
            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..3123
                     /organism="Providencia stuartii"
                     /mol_type="genomic DNA"
                     /strain="CAVP496"
                     /isolation_source="human"
                     /host="Homo sapiens"
                     /db_xref="taxon:588"
                     /plasmid="pCAVP496-3123"
                     /geo_loc_name="USA: Virginia"
                     /collected_by="University of Virginia Health System"
     gene            740..1288
                     /locus_tag="P2E04_RS21500"
                     /old_locus_tag="P2E04_21500"
     CDS             740..1288
                     /locus_tag="P2E04_RS21500"
                     /old_locus_tag="P2E04_21500"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001722544.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="helix-turn-helix domain-containing protein"
                     /protein_id="WP_257766363.1"
                     /translation="MQSVTVATETQRRIRQRELAAADEKEAQEREEARKNKGFTQVYSK
                     GWRRVRELSKGNAGAAGLYAFFAEHIDPTCGAVVCDQQFLADHLEVSTRTIRNWLKYLE
                     TERALVRIPVAGRVCAYALDPHEVWKGYDNAKEYAAFVTKTLVNKDGDIKRRIMSMFSP
                     EERPDDRDTDTLDMFGDQP"
                     /name="helix-turn-helix domain-containing protein"
     gene            1285..1488
                     /locus_tag="P2E04_RS22125"
                     /old_locus_tag="P2E04_21505"
     CDS             1285..1488
                     /locus_tag="P2E04_RS22125"
                     /old_locus_tag="P2E04_21505"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000131876.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_000131876.1"
                     /translation="MTDPLKALFGKPDYSHIVRDTTATISITAAEMAAVLEAYDRGIDT
                     LDGTTRTALDSVISKLKDEVWP"
                     /name="hypothetical protein"
     gene            1479..1700
                     /locus_tag="P2E04_RS22130"
                     /old_locus_tag="P2E04_21510"
     CDS             1479..1700
                     /locus_tag="P2E04_RS22130"
                     /old_locus_tag="P2E04_21510"
                     /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_001251694.1"
                     /translation="MAMSMYYIKTGLEYWKPKGYGYTKSREEAGVFTLKDMEELNLDGC
                     TLERAEVAFLDEDGPSPDLPHRVTLPRD"
                     /name="hypothetical protein"
     gene            1783..1938
                     /locus_tag="P2E04_RS21515"
                     /old_locus_tag="P2E04_21515"
     CDS             1783..1938
                     /locus_tag="P2E04_RS21515"
                     /old_locus_tag="P2E04_21515"
                     /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_001736727.1"
                     /translation="MPVNPRDYCQPLHPGCLGLVESGLGLVESGLMLVKQWFKVVQGWL
                     KLVEKG"
                     /name="hypothetical protein"
     gene            complement(1935..2921)
                     /gene="mobV"
                     /locus_tag="P2E04_RS21520"
                     /old_locus_tag="P2E04_21520"
     CDS             complement(1935..2921)
                     /gene="mobV"
                     /locus_tag="P2E04_RS21520"
                     /old_locus_tag="P2E04_21520"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000852935.1"
                     /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_276123118.1"
                     /translation="MAFAIMRAKKLNSMGTVAAALQHCYRDRETPNADQERTPDNVHLA
                     ARSTDEAMGQLRERLPEKRRKDAVLAVEYVMSASPEWWQTASADQQREFFKRSTEWLAD
                     KYGAENVVTATIHRDELTPHLSAFVVPRTADGRLSAKEFIGNRTKMSQDQTSYAERVAD
                     LGLERGIEGSRATHQRVKTHYGAIQQAGRDVPHLTPDELKPQKVKGVSLAEKVFGAVET
                     VEGVAQRLNAKIMGSVQPMAEKAAVSAQNERRAKELRETLAQQQKRLQALQEPFKGLSK
                     DQVAGLIRQAVKLRQENEQEKQERAQQIKERFKAKRERERSDRSRGR"
                     /name="mobV"
ORIGIN
        1 ccccaaaccc cgcgttcgcc acgtggcagg ggtgcaggtg gccgcgccgc ttcgctctgc
       61 tctacctgcc cccttgcctg agcgtggggg tcactccatc acgtcaaggg ttcgcttcgc
      121 cgggtgctca cccgatccct tccgcttcgc tccagggctg cggcttccgc tcccgccctt
      181 gacctgattc cgttccgagt ggaggcagcg tcaaggggtc gtggaatacc gcaaggcgcg
      241 cagcgcctga ggatatgccg cgaaagcccc ttgacgctgc cggaacgacc cagcctctgg
      301 ctctggggtt gggaacgaag ggagcgcagc gaccgcaggc cccagccccc gagcctcacg
      361 gcggcgagtg tggggagtcc agaggggcaa agcccctttg ggcctagcgc agcggaaaca
      421 aaccctctcg cctctggcga ggcattaact ccaagggagc gcagcgaccg tcagcagggt
      481 gccaagcgaa gcgccggcgg gacggcagtc ccttagagga gaaggggaaa aatactaaat
      541 gattgattta tatagttttt aaattttgtg ataggaaacg tagggttccg gacaaccgga
      601 agcagcttgt ttccgcttac ttcctatcat aggaaacaaa ttgcttgact tgggaaacgg
      661 ttttgggaaa taattttcct atggtaggaa ttaaacgtcc ggttaagcgg acgccctgtt
      721 tccggttagg aggtcaacaa tgcaaagcgt caccgtagcg acagagacac agagacgaat
      781 caggcaaagg gagctggcag cagcagacga gaaggaggct caggagcgcg aggaggcgcg
      841 aaagaacaag gggttcacac aggtatattc aaagggatgg cggcgcgtca gggagctgtc
      901 aaagggcaat gcgggggccg ctggcctgta tgccttcttc gctgaacaca tcgaccctac
      961 ctgtggcgct gttgtctgcg atcagcagtt cctggctgac catctggagg ttagcacccg
     1021 cacgattcgg aactggctca agtaccttga gacagaacgc gccttggtca gaatcccagt
     1081 cgctgggcgg gtttgcgcct acgctcttga cccccacgag gtctggaaag ggtacgacaa
     1141 cgccaaagaa tacgcggcct tcgtgaccaa gacgctggtc aacaaggacg gcgatattaa
     1201 gcgccggatc atgtcgatgt ttagcccaga ggaacgccca gacgacaggg atacagacac
     1261 gcttgatatg tttggagatc agccatgaca gatccactca aagccctttt cggcaagcct
     1321 gattactccc atatcgtaag ggacaccacg gccactatca gcatcacagc cgctgaaatg
     1381 gccgctgttt tggaggctta cgacaggggt atagacacgc tggacggcac caccagaacg
     1441 gcgctggatt ccgttatatc gaaactcaag gacgaggtat ggccatgagc atgtattaca
     1501 tcaagacagg tctggagtac tggaaaccca agggctacgg gtacaccaag agccgcgagg
     1561 aggcgggggt tttcaccctc aaggacatgg aagaattgaa cctcgatggc tgcaccctgg
     1621 aacgcgccga agtggcgttc ctggacgagg acggccccag tcccgaccta ccccaccgcg
     1681 tcaccctgcc ccgcgattga gcggggcgct ggagggtttc aaaggggcac cctttggcac
     1741 gggatatgtg tcaaaaacgg agtttttgta aacatatccg acgtgcctgt aaatccgcgc
     1801 gattactgcc aacccttaca ccccggttgc ttagggttgg ttgaaagtgg tttagggttg
     1861 gttgaaagtg gtttaatgtt ggttaaacaa tggtttaagg ttgttcaagg ttggttaaag
     1921 ttggttgaaa agggttaacg gcccctgctg cggtcgctgc gctcccgttc ccgcttggcc
     1981 ttgaatcgct ctttgatctg ctgggcgcgc tcctgcttct cctgctcgtt ctcctgccgc
     2041 aatttcaccg cctgccggat cagtcccgct acctgatcct tggatagccc cttaaacggc
     2101 tcctgaaggg cctgtaagcg tttttgctgc tgggctaggg tttcccttag ctccttggct
     2161 cttcgctcgt tctgggcgct tacagcggct ttctcggcca tcggctgcac agaccccatt
     2221 attttggcgt tcaacctttg cgccacccct tcgaccgtct ccacggctcc gaacaccttc
     2281 tcggccagtg acaccccctt gaccttctgg ggtttcagct cgtcaggcgt caggtgtggc
     2341 acgtctcggc ctgcctgctg gatcgcccca tagtgggttt taactcgctg gtgtgtggcc
     2401 ctgctgccct cgatgccccg ttcaagcccc agatcggcca cccgttcggc gtagctggtc
     2461 tggtcctggc tcatcttcgt ccggttgcca atgaactcct tggcactcag gcgcccgtca
     2521 gccgtccgag gcaccacgaa cgccgacagg tgcggggtca gctcatcccg gtggatcgtg
     2581 gccgtgacca cgttctcagc gccgtacttg tcggccagcc actcggtcga tcgcttgaag
     2641 aactcccgct gctggtcggc gcttgcggtc tgccaccact ccggcgaggc gctcatcacg
     2701 tattcgaccg ccagcaccgc atccttgcgg cgcttctccg gcagcctctc cctgagctgg
     2761 cccatcgcct catcggtcga tctggccgcc aggtgaacgt tgtccggtgt gcgctcctga
     2821 tcggcgttcg gcgtctcgcg gtcgcggtag cagtgctgca acgcagccgc caccgtgccc
     2881 atgctgttga gcttcttcgc cctcatgatc gcaaacgcca tccgtccccc tccgcactgt
     2941 cagattgctg ccagcccgtc gaggtacgaa tgtgcctccg gcgggccact tctttgaagt
     3001 gtactcacta gactttactt cgtaaagtac gtgaccgcta cgcggttgca gcggcctgcg
     3061 gccttgctct acgggcttcg ccctgcgcct cccttcggtc gttgcgaaca ccttggggcg
     3121 ctg
//
