LOCUS       NZ_CP095445             2683 bp    DNA     circular CON 11-MAR-2024
DEFINITION  Providencia stuartii strain CMC-4104 plasmid pSmall, complete
            sequence.
ACCESSION   NZ_CP095445
VERSION     NZ_CP095445.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN27484493
            Assembly: GCF_023547145.1
KEYWORDS    RefSeq.
SOURCE      Providencia stuartii
  ORGANISM  Providencia stuartii
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Morganellaceae; Providencia.
REFERENCE   1  (bases 1 to 2683)
  AUTHORS   Jensen,R.V., Todd,S.M., Lahmers,K., Stornelli,N.K., Everson,N.A.,
            McDaniel,L.F., De La Espriella,M.G., Faulhaber,J.R. and Rao,J.
  TITLE     Multiple Copies of NDM-1 Multi-drug Resistance Genes in a Clinical
            Isolate of Providencia stuartii
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 2683)
  AUTHORS   Jensen,R.V., Todd,S.M., Lahmers,K., Stornelli,N.K., Everson,N.A.,
            McDaniel,L.F., De La Espriella,M.G., Faulhaber,J.R. and Rao,J.
  TITLE     Direct Submission
  JOURNAL   Submitted (08-APR-2022) Biological Sciences, Virginia Tech, 970
            Washington Street, Room 119, Blacksburg, VA 24061, USA
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Date                     :: 2022
            Assembly Method :: Flye v. MARCH-2022; Geneious v. Prime 2022.02
            Assembly Name                     :: CMC_Pro_4104
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 70.0x
            Sequencing Technology :: Oxford Nanopore MinION; Illumina NextSeq
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_023547145.1-RS_2024_03_11
            Annotation Date                   :: 03/11/2024 12:57:32
            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)                     :: 4,583
            CDSs (total)                      :: 4,475
            Genes (coding)                    :: 4,342
            CDSs (with protein)               :: 4,342
            Genes (RNA)                       :: 108
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 80
            ncRNAs                            :: 6
            Pseudo Genes (total)              :: 133
            CDSs (without protein)            :: 133
            Pseudo Genes (ambiguous residues) :: 0 of 133
            Pseudo Genes (frameshifted)       :: 59 of 133
            Pseudo Genes (incomplete)         :: 96 of 133
            Pseudo Genes (internal stop)      :: 24 of 133
            Pseudo Genes (multiple problems)  :: 39 of 133
            CRISPR Arrays                     :: 4
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP095445.1.
            Bacteria and source DNA available from Dr. Jayasimha Rao, Virginia
            Tech Carilion School of Medicine, 101 Elm Ave, 4th Floor, Roanoke,
            VA 24013.
            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="CMC-4104"
                     /isolation_source="Splenic fine needle aspirate"
                     /host="Homo sapiens"
                     /db_xref="taxon:588"
                     /plasmid="pSmall"
                     /geo_loc_name="USA: Roanoke, VA"
                     /lat_lon="37.271 N 79.9414 W"
                     /collection_date="2021-05-12"
                     /collected_by="Carilion Roanoke Memorial Hospital"
     gene            101..541
                     /locus_tag="MWH14_RS22890"
                     /old_locus_tag="MWH14_22890"
     CDS             101..541
                     /locus_tag="MWH14_RS22890"
                     /old_locus_tag="MWH14_22890"
                     /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            1502..2146
                     /locus_tag="MWH14_RS22895"
                     /old_locus_tag="MWH14_22895"
     CDS             1502..2146
                     /locus_tag="MWH14_RS22895"
                     /old_locus_tag="MWH14_22895"
                     /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             1503..2143
                     /name="qnrD1"
                     /gene="qnrD1"
                     /gene_name="quinolone resistance pentapeptide repeat
                     protein QnrD1"
                     /tool="amrfinderplus"
                     /drug_class="QUINOLONE"
                     /identity="100.0"
                     /coverage="100.0"
     Typing          1253..1408
                     /name="Col3M"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="98.089"
                     /coverage="100.0"
                     /evalue="2.29e-71"
ORIGIN
        1 aacgctcgcc gcaaggcgtg aacttgtttc acgtcgagga agcggaattt ctcgaaagcc
       61 ttatactgtc tccgttcaca catgatcgga gggtgtctct atgtctcaat tatttcgttt
      121 ggcatcgcca gaagattacg aatacatcga agaattaaat ttatgggaat tgtcatttga
      181 taagcgaccg gttcaagggg ttcgttgtga agatccggtg atcggggcag aaaaatataa
      241 tcaagggcgt gaaaaattta aggcgttagc gtcacggcat aaaaaacact ggaaaccgaa
      301 cggattgacc ttttcggagt tgatccgctg ggcaatagaa tgcggaactc cagaacaatg
      361 tcagcttgtt ttagcgttat accattgcac aaacgatgat gattatcagg cgatgggaat
      421 tcagttaagc cgaagtattg ataatgcaaa tgtcagtccg atcatctttt tcacaggtaa
      481 aaatcaacgg ttattaggtg atatttcgat gctaaaacag ctcgaagaaa aggtgcgctg
      541 acgttaggtt tacctattat tttatgtatt atcctatcta ttattctatc tcttatttta
      601 tctatttcgt ctgtaatagg tagaataata catagaataa gatacagaat aatagataga
      661 cacaagatga cgttgtgtta tttcttaccc attaatccac ctgttattct acctattact
      721 ttacccgtta ttgcacccaa tttaggtata acgggcagaa taacgggtga aataatgggt
      781 agaatcatag ttttactaac ttgcacccca tgatactttc agtatcaatg ccactcattt
      841 tctggacgaa aatgaatgac ataaggctcc gccctctggc tattttcttc ggctggacgc
      901 ctgcgaaaaa aaccattcac ccaagcccgt caaactcact gcgttcgtct gaccaccccc
      961 ttttttcgcc cctgtatttg gtcgctcaaa aatgtggtgg tcagacgctt cgcttgacgg
     1021 ggggctttgc ccccaaaacg aaacacgttc actggggttc acttgccatc gctggggcgt
     1081 gtcatttcgt ttcggctccc cctgtttttc cctttcttcg ctggacgctc atcaggataa
     1141 aaacaaaaag cctaccgccc tcgttttact cggttggtca aatcgcttct tgccacaaaa
     1201 caagtttgtg actttcagcg atttcgcatc gttttacttg tcagtttgca cgatgttaaa
     1261 aacgcactca gaagcccgca aaaccgttct aaactttcag cgtagatttg ggtgttttat
     1321 agggtgatcg tgtcttaaaa tcgtttcgag gggctttaat ggggatgaac gggaggtttt
     1381 tgctaactaa ctcgcccgtt taacataaaa gggattgtat gaatcaattt tagctagagt
     1441 ttaaggttgt tcaaattaat gtacaatgat tgcactgtat aaataaccag gtgtagcatg
     1501 tatggaaaag cactttatca atgaaaagtt ttcacgagat caatttacgg ggaatagagt
     1561 taaaaatatt gccttttcaa attgtgattt ttcaggggtt gatttaactg atactgaatt
     1621 tgttgattgt agtttttacg acaggaatag cttggaaggg tgtgatttta atagagccaa
     1681 actaaaaaac gctagcttta aaagctgcga tttatcaatg agtaatttta aaaacattag
     1741 cgccttaggt cttgaaatta gtgagtgttt agctcaagga gctgattttc gaggggctaa
     1801 ttttatgaat atgataacta caaggtcatg gttttgtagt gcttatataa ccaagacaaa
     1861 tcttagttac gctaattttt ctagagtcat attagaaaag tgcgaactgt gggaaaatcg
     1921 ctggaatggc actgtgataa ctggcgccgt gtttcgtggc tccgatcttt cttgtgggga
     1981 gttttcatcg tttgattggt ctttggctga ttttactggt tgtgatttaa cgggtggggc
     2041 gcttggcgag cttgatgcaa ggcgaattaa tttagatgga gtgaagttgg atggagagca
     2101 ggcgcttcag cttgttgaga gtttaggtgt tattgttcac cgataaaatc taggtaaaaa
     2161 acgcctaatg ccccaatgtg gtactaatca aaacggagcg aagcgacatc ttcatcttgt
     2221 ctttgctttt ctccatgatc agttattggg tcatggtctc ttagctcgtt aatctggcta
     2281 agtttggtta ggttgggctt ctttcgacac ttcgcaatcc aagaaatccc tagtccgttg
     2341 attggtgctc ttatcaggta cgcactgtaa tctttcgata ccgcagcgtg attcggaggt
     2401 agagccggaa tttcgttttc cggtacgttt tactaccaca atttgcctgt ttatcctttc
     2461 ggagaccggg ctaagtccga gtcaatcaag tggtgcattt gggttaatgt cgttggctgg
     2521 tatttaatga gaacgtgaca agcgcctctc acgttgctaa gattggattg cgacgtctaa
     2581 tctgagcaac gaatgcacaa gatttagagt accagagccc tgtgatgctg tcacggggct
     2641 ttgttacatc tggagcttgg taaacctcat aaattcaatt cgc
//
