LOCUS       NZ_CP141744             2683 bp    DNA     circular CON 21-APR-2024
DEFINITION  Providencia rettgeri strain 2023CK-01506 plasmid unnamed2, complete
            sequence.
ACCESSION   NZ_CP141744
VERSION     NZ_CP141744.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN38788851
            Assembly: GCF_034330845.1
KEYWORDS    RefSeq.
SOURCE      Providencia rettgeri
  ORGANISM  Providencia rettgeri
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Morganellaceae; Providencia.
REFERENCE   1  (bases 1 to 2683)
  AUTHORS   Hergert,J., Casey,R., Wagner,J., Young,E.L. and Oakeson,K.F.
  TITLE     Pathogen: clinical or host-associated sample
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 2683)
  AUTHORS   Hergert,J., Casey,R., Wagner,J., Young,E.L. and Oakeson,K.F.
  TITLE     Direct Submission
  JOURNAL   Submitted (20-DEC-2023) Utah Public Health Laboratory, Utah Public
            Health Laboratory Infectious Disease submission group, 4431 S 2700
            W, Salt Lake City, UT 84129, USA
REFERENCE   3  (bases 1 to 2683)
  CONSRTM   Clinical and Environmental Microbiology Branch: Whole genome
            sequencing antimicrobial resistance pathogens in the healthcare
            setting
  TITLE     Direct Submission
  JOURNAL   Submitted (12-DEC-2023) Division of Healthcare Quality Promotion, US
            Centers for Disease Control and Prevention, 1600 Clifton Rd,
            Atlanta, GA, USA
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: Unicycler v. 0.5.0
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 20.0x
            Sequencing Technology :: Illumina MiSeq; Oxford Nanopore GridION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_034330845.1-RS_2024_04_21
            Annotation Date                   :: 04/21/2024 14:07:35
            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)                     :: 4,297
            CDSs (total)                      :: 4,191
            Genes (coding)                    :: 4,136
            CDSs (with protein)               :: 4,136
            Genes (RNA)                       :: 106
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 80
            ncRNAs                            :: 4
            Pseudo Genes (total)              :: 55
            CDSs (without protein)            :: 55
            Pseudo Genes (ambiguous residues) :: 0 of 55
            Pseudo Genes (frameshifted)       :: 14 of 55
            Pseudo Genes (incomplete)         :: 42 of 55
            Pseudo Genes (internal stop)      :: 9 of 55
            Pseudo Genes (multiple problems)  :: 9 of 55
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP141744.1.
            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 rettgeri"
                     /mol_type="genomic DNA"
                     /strain="2023CK-01506"
                     /isolation_source="Wound/Abscess"
                     /host="Homo sapiens"
                     /db_xref="taxon:587"
                     /plasmid="unnamed2"
                     /geo_loc_name="USA"
                     /collection_date="2023-10-27"
     gene            159..599
                     /locus_tag="VNI59_RS21480"
                     /old_locus_tag="VNI59_21480"
     CDS             159..599
                     /locus_tag="VNI59_RS21480"
                     /old_locus_tag="VNI59_21480"
                     /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            1560..2204
                     /locus_tag="VNI59_RS21485"
                     /old_locus_tag="VNI59_21485"
     CDS             1560..2204
                     /locus_tag="VNI59_RS21485"
                     /old_locus_tag="VNI59_21485"
                     /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             1561..2201
                     /name="qnrD1"
                     /gene="qnrD1"
                     /gene_name="quinolone resistance pentapeptide repeat
                     protein QnrD1"
                     /tool="amrfinderplus"
                     /drug_class="QUINOLONE"
                     /identity="100.0"
                     /coverage="100.0"
     Typing          1311..1466
                     /name="Col3M"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="98.089"
                     /coverage="100.0"
                     /evalue="2.29e-71"
ORIGIN
        1 tgctgtcacg gggctttgtt acatctggag cttggtaaac ctcataaatt caattcgcaa
       61 cgctcgccgc aaggcgtgaa cttgtttcac gtcgaggaag cggaatttct cgaaagcctt
      121 atactgtctc cgttcacaca tgatcggagg gtgtctctat gtctcaatta tttcgtttgg
      181 catcgccaga agattacgaa tacatcgaag aattaaattt atgggaattg tcatttgata
      241 agcgaccggt tcaaggggtt cgttgtgaag atccggtgat cggggcagaa aaatataatc
      301 aagggcgtga aaaatttaag gcgttagcgt cacggcataa aaaacactgg aaaccgaacg
      361 gattgacctt ttcggagttg atccgctggg caatagaatg cggaactcca gaacaatgtc
      421 agcttgtttt agcgttatac cattgcacaa acgatgatga ttatcaggcg atgggaattc
      481 agttaagccg aagtattgat aatgcaaatg tcagtccgat catctttttc acaggtaaaa
      541 atcaacggtt attaggtgat atttcgatgc taaaacagct cgaagaaaag gtgcgctgac
      601 gttaggttta cctattattt tatgtattat cctatctatt attctatctc ttattttatc
      661 tatttcgtct gtaataggta gaataataca tagaataaga tacagaataa tagatagaca
      721 caagatgacg ttgtgttatt tcttacccat taatccacct gttattctac ctattacttt
      781 acccgttatt gcacccaatt taggtataac gggcagaata acgggtgaaa taatgggtag
      841 aatcatagtt ttactaactt gcaccccatg atactttcag tatcaatgcc actcattttc
      901 tggacgaaaa tgaatgacat aaggctccgc cctctggcta ttttcttcgg ctggacgcct
      961 gcgaaaaaaa ccattcaccc aagcccgtca aactcactgc gttcgtctga ccaccccctt
     1021 ttttcgcccc tgtatttggt cgctcaaaaa tgtggtggtc agacgcttcg cttgacgggg
     1081 ggctttgccc ccaaaacgaa acacgttcac tggggttcac ttgccatcgc tggggcgtgt
     1141 catttcgttt cggctccccc tgtttttccc tttcttcgct ggacgctcat caggataaaa
     1201 acaaaaagcc taccgccctc gttttactcg gttggtcaaa tcgcttcttg ccacaaaaca
     1261 agtttgtgac tttcagcgat ttcgcatcgt tttacttgtc agtttgcacg atgttaaaaa
     1321 cgcactcaga agcccgcaaa accgttctaa actttcagcg tagatttggg tgttttatag
     1381 ggtgatcgtg tcttaaaatc gtttcgaggg gctttaatgg ggatgaacgg gaggtttttg
     1441 ctaactaact cgcccgttta acataaaagg gattgtatga atcaatttta gctagagttt
     1501 aaggttgttc aaattaatgt acaatgattg cactgtataa ataaccaggt gtagcatgta
     1561 tggaaaagca ctttatcaat gaaaagtttt cacgagatca atttacgggg aatagagtta
     1621 aaaatattgc cttttcaaat tgtgattttt caggggttga tttaactgat actgaatttg
     1681 ttgattgtag tttttacgac aggaatagct tggaagggtg tgattttaat agagccaaac
     1741 taaaaaacgc tagctttaaa agctgcgatt tatcaatgag taattttaaa aacattagcg
     1801 ccttaggtct tgaaattagt gagtgtttag ctcaaggagc tgattttcga ggggctaatt
     1861 ttatgaatat gataactaca aggtcatggt tttgtagtgc ttatataacc aagacaaatc
     1921 ttagttacgc taatttttct agagtcatat tagaaaagtg cgaactgtgg gaaaatcgct
     1981 ggaatggcac tgtgataact ggcgccgtgt ttcgtggctc cgatctttct tgtggggagt
     2041 tttcatcgtt tgattggtct ttggctgatt ttactggttg tgatttaacg ggtggggcgc
     2101 ttggcgagct tgatgcaagg cgaattaatt tagatggagt gaagttggat ggagagcagg
     2161 cgcttcagct tgttgagagt ttaggtgtta ttgttcaccg ataaaatcta ggtaaaaaac
     2221 gcctaatgcc ccaatgtggt actaatcaaa acggagcgaa gcgacatctt catcttgtct
     2281 ttgcttttct ccatgatcag ttattgggtc atggtctctt agctcgttaa tctggctaag
     2341 tttggttagg ttgggcttct ttcgacactt cgcaatccaa gaaatcccta gtccgttgat
     2401 tggtgctctt atcaggtacg cactgtaatc tttcgatacc gcagcgtgat tcggaggtag
     2461 agccggaatt tcgttttccg gtacgtttta ctaccacaat ttgcctgttt atcctttcgg
     2521 agaccgggct aagtccgagt caatcaagtg gtgcatttgg gttaatgtcg ttggctggta
     2581 tttaatgaga acgtgacaag cgcctctcac gttgctaaga ttggattgcg acgtctaatc
     2641 tgagcaacga atgcacaaga tttagagtac cagagccctg tga
//
