LOCUS       NZ_CP119556             3223 bp    DNA     circular CON 11-MAR-2024
DEFINITION  Providencia stuartii strain CAVP450 plasmid pCAVP450-3223, complete
            sequence.
ACCESSION   NZ_CP119556
VERSION     NZ_CP119556.1
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 3223)
  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  JOURNAL   Unpublished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 3223)
  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
            CP119556.1.
            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..3223
                     /organism="Providencia stuartii"
                     /mol_type="genomic DNA"
                     /strain="CAVP450"
                     /isolation_source="human"
                     /host="Homo sapiens"
                     /db_xref="taxon:588"
                     /plasmid="pCAVP450-3223"
                     /geo_loc_name="USA: Virginia"
                     /collected_by="University of Virginia Health System"
     gene            join(3071..3223,1..63)
                     /locus_tag="P2E06_RS21495"
                     /old_locus_tag="P2E06_21495"
     CDS             join(3071..3223,1..63)
                     /locus_tag="P2E06_RS21495"
                     /old_locus_tag="P2E06_21495"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000137421.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MbeD family mobilization/exclusion protein"
                     /protein_id="WP_024195375.1"
                     /translation="MTELEKQLLSALEQLQQDYSKRLDEWENAFAEWRTMSGLIQRENA
                     ALNERVTVLSRQVQSLSEQLRRLSKG"
                     /name="MbeD family mobilization/exclusion protein"
     gene            231..563
                     /locus_tag="P2E06_RS21500"
                     /old_locus_tag="P2E06_21500"
     CDS             231..563
                     /locus_tag="P2E06_RS21500"
                     /old_locus_tag="P2E06_21500"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_008784643.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="EmrE family multidrug efflux SMR transporter"
                     /protein_id="WP_001099531.1"
                     /translation="MNTYIFLGGAIVAEVIGTTFMKYSEGFTRLWPSVGTAISYCAAFY
                     LLSQTLENIPTGIAYAIWSGAGIVLISLAGWLVSGQKLDWPAIAGMFLICVGVLVINIF
                     SKSSAH"
                     /name="EmrE family multidrug efflux SMR transporter"
     gene            1581..1904
                     /locus_tag="P2E06_RS21505"
                     /old_locus_tag="P2E06_21505"
     CDS             1581..1904
                     /locus_tag="P2E06_RS21505"
                     /old_locus_tag="P2E06_21505"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000957083.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MobC family plasmid mobilization relaxosome
                     protein"
                     /protein_id="WP_004193914.1"
                     /translation="MLTMWVTEDEHRRLLERCEGKQLAAWMRQTCLDEKPARAGKLPSI
                     SPALLRQLAGMGNNLNQIARQVNAGGGSGHDRVQIVAALMAIDAGLERLRHAVLEKGAD
                     DDR"
                     /name="MobC family plasmid mobilization relaxosome protein"
     gene            2113..>2547
                     /locus_tag="P2E06_RS21510"
                     /old_locus_tag="P2E06_21510"
                     /pseudo=""
     CDS             2113..>2547
                     /locus_tag="P2E06_RS21510"
                     /old_locus_tag="P2E06_21510"
                     /inference="COORDINATES: protein motif:HMM:NF015397.4"
                     /note="incomplete; partial in the middle of a contig;
                     missing C-terminus; Derived by automated computational
                     analysis using gene prediction method: Protein Homology."
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="relaxase/mobilization nuclease domain-containing
                     protein"
                     /name="relaxase/mobilization nuclease domain-containing
                     protein"
     gene            2582..3067
                     /locus_tag="P2E06_RS21515"
                     /old_locus_tag="P2E06_21515"
     CDS             2582..3067
                     /locus_tag="P2E06_RS21515"
                     /old_locus_tag="P2E06_21515"
                     /inference="COORDINATES: protein motif:HMM:NF016710.4"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MbeB family mobilization protein"
                     /protein_id="WP_025367738.1"
                     /translation="MNSLLTLAKDLEQKSKAQQQTTGEMLKAAFSEHEKSVRAELSESE
                     KRISAAILDHDRKLSSAMSQRTKGMLRMVSQTWLTIVLVSALLIASSAGILWWQGQQIL
                     ENYTTIREQKSTQAMLSERNSGVQLSTCGEQRRRCVRVNPEAGQFGEDSSWMILAGK"
                     /name="MbeB family mobilization protein"
     ARG             232..563
                     /name="qacG"
                     /gene="qacG"
                     /gene_name="small multidrug resistance (SMR) antibiotic
                     efflux pump"
                     /tool="rgi"
                     /drug_class="disinfecting agents and antiseptics"
                     /identity="41.35"
                     /coverage="102.8"
     Typing          1294..1485
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="92.308"
                     /coverage="89.0"
                     /evalue="3.38e-71"
     Typing          complement(831..1311)
                     /name="ColRNAI_rep_cluster_1987"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="84.867"
                     /coverage="93.0"
                     /evalue="1.73e-132"
     Typing          1895..3222
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="93.454"
                     /coverage="99.0"
                     /evalue="0.0"
ORIGIN
        1 acggtcttga gcaggcaggt gcagagtttg agcgagcagc tgcgccggtt gtcgaaaggc
       61 tgaacgcgat agaaactcac cggcagcagg agcgggcggt gcagcaccag aaagcgctgg
      121 agctggaacg atcgcagtgg cagcatcatg gtccttcgct atgataagcc gggttctatt
      181 aattagttgt tatgtaaaga tatttaaatt tttcaacatg aggtattttt atgaatacat
      241 atattttcct gggaggggct attgtggctg aagtcatagg caccaccttt atgaaatatt
      301 cagaaggatt tacacgcctg tggccgtctg taggaactgc aataagttat tgcgctgcct
      361 tttatctgct ttcccaaaca ttggaaaata tacctaccgg tattgcttac gcaatttggt
      421 ctggtgcggg aattgtacta ataagcctag ctggttggtt ggttagcggt caaaaacttg
      481 attggcccgc aattgcagga atgttcctta tttgcgttgg agttttggtt attaatattt
      541 tttcaaaatc ttctgcgcat taacttttta ccgaagcata ttggccaaag caaaaggatt
      601 tccttgagat cctttctttc tgcgcgtaat ctttttccct gtaaacaaaa aaaccaccgc
      661 taccaacggt ggttcgtttg ccggaattca gagctaccaa ctctttgttc cgatggtaac
      721 tggctttcac ggagcgcaga tacctaaact gtcctttcag tgtagccgca ctcaggcttt
      781 cacttcaaga actctgtagg cattctctac aatctctgct ccgtgaaccc agttaccaat
      841 ggctaccgcc actggcgatt tgtcgtgtct ttccgggttg gactcaagtt gatagttacc
      901 ggaacgggcg tggtagtcgg actgaacggg gggttcgtgc atacagtcca tcctggagcg
      961 aactgcctac ccggaaccga gtttcaggcg tggaatgaga aaccgcggcc ataacagcgg
     1021 aatgacaccg gtaaaccgaa aggcaggaat gcgggggagc acgagggagc caccaggggg
     1081 aaacgcctgg tatctttaag ccgcatcggg tttcgccacc gctgatttga gcgtcatttt
     1141 cgtgatactc gtcagggggg cggagcctat ggaaaaacgg caactccgca tccttttctt
     1201 ggcctttcct gcttcgagcg gcatttgctt atcccgtaat ctgtgagctg gtaacgcccg
     1261 ccgcagtctc acggcaggag cgtagcgacc gagtgagcga ggaggcgtca tttcatcacc
     1321 acctgcattt tgcacttacg cccggcagcc gcatttttcc cctgtcacat gaagcacttt
     1381 cataaattgc cactccgtca taacatgttt agccagtata cactccgcta gcgctacgtg
     1441 actggttcag ggctgcgccc cgaaacccgc taaaaccact gccgcgcctg cggcttgtcc
     1501 aacaccgtgc cgaccgggaa aagatttccc gtccgtcccg gcgttatcag gaggccggat
     1561 tggcagacaa acgcagcaaa atgctcacca tgtgggtgac tgaggacgag caccggcgtc
     1621 tgctggagcg ctgcgagggt aagcaactcg cggcctggat gcggcagacg tgcctggacg
     1681 agaagcccgc acgcgccggc aaacttccgt cgatctcgcc ggcgctgctt cgtcagcttg
     1741 ccggcatggg gaacaacctt aaccagattg cccgccaggt taacgccggt ggtggaagcg
     1801 gacacgaccg cgtgcagatt gtcgccgcgc tgatggccat cgatgccgga ctcgagcggt
     1861 tgcggcatgc cgtactggaa aagggtgctg atgatgatcg ttaagtttca tcctcggggg
     1921 cgcggcggcg gcggcgggcc ggtcgattat ctgctgggta aagatcgcca gcgcgacggc
     1981 gccagcgttc tgcaggggaa gccggatgaa gtccgggagc ttatcgacgc ctcgccctac
     2041 gccaaaaagt acacttccgg cgttctgtct tttgccgaac aggatttacc gcccggccag
     2101 cgcgaaaagc tgatggcgag tttcgagcgg gttctgatgc ccggactcga taaagaccag
     2161 tacagcgtgc tgtgggttga gcaccgggac aaggggcggc tggagctgaa cttcctgatc
     2221 ccgaacacgg agcttctgac cggcaagcgg ctacagccgt attacgaccg cgccgaccgt
     2281 ccgcgcatcg atgcctggca gaccatagtg aacggcaggc tggggctgca tgacccgaac
     2341 gcgccggaga accggcgggt gctggtctcg ccttccgcgc tgccggaagc gaagcaggaa
     2401 gccgcccagg cgattacgag cggcctgctt gcccttgcct catccgggga gctgaaaacg
     2461 cgtcaggacg tcactgaggc gctggaaagc gcaggttttg aggtggtgcg caccacaaaa
     2521 agcagcatca gcattgccga cccggacggg gggcgaaaca tccgactgaa gggagccatc
     2581 tatgaacagt cttttaacgc tggcgaagga cttagagcag aaatcgaaag cgcagcagca
     2641 gactaccggc gagatgctga aagccgcatt cagcgagcac gagaagtctg tcagagcgga
     2701 actgagcgaa agcgagaaga gaatcagcgc cgccatcctc gaccacgacc ggaagctgtc
     2761 ctcagccatg agccagcgca cgaaagggat gctgcgcatg gtcagccaga cgtggctgac
     2821 catcgttctg gtctccgcgc tgctgatagc gtcgagcgcg ggcattctgt ggtggcaggg
     2881 gcagcagata ctcgagaact atacgaccat ccgggagcag aagagcacgc aggccatgct
     2941 gtcagagagg aacagcggcg tacagctctc gacctgcggc gagcagagac gccgctgcgt
     3001 gagggtgaac ccggaagcgg gacagttcgg agaggactcg agctggatga tactggcggg
     3061 gaaatagcac atgacggagc tggaaaaaca gttgctgagc gcattagagc agctacagca
     3121 ggactactcg aaaaggctgg acgagtggga gaacgccttc gcggaatggc ggacgatgtc
     3181 tggtcttatt caacgggaga acgcggcgct gaacgagcgc gtc
//
