LOCUS       NZ_CP123254             2683 bp    DNA     circular CON 11-MAR-2024
DEFINITION  Providencia rettgeri strain YZLc5-3 plasmid pYZLc5-3_2k, complete
            sequence.
ACCESSION   NZ_CP123254
VERSION     NZ_CP123254.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN30724597
            Assembly: GCF_025583505.2
KEYWORDS    RefSeq.
SOURCE      Providencia rettgeri
  ORGANISM  Providencia rettgeri
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Morganellaceae; Providencia.
REFERENCE   1  (bases 1 to 2683)
  AUTHORS   Yin,Y.
  TITLE     Transmission Patterns of Multiple NDM Variants Producing Strains in
            Animal and Environment Settings from Live Poultry Market
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 2683)
  AUTHORS   Yin,Y.
  TITLE     Direct Submission
  JOURNAL   Submitted (29-MAR-2023) College of Veterinary Medicine, Yangzhou
            University, 48 Wenhui East Road, Yangzhou, Jiangsu 225009, China
REFERENCE   3  (bases 1 to 2683)
  AUTHORS   Yin,Y.
  TITLE     Direct Submission
  JOURNAL   Submitted (08-SEP-2022) College of Veterinary Medicine, Yangzhou
            University, 48 Wenhui East Road, Yangzhou, Jiangsu 225009, China
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: Unicycler v. v0.4.8
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 100.0x
            Sequencing Technology             :: Oxford Nanopore MinION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_025583505.2-RS_2024_03_11
            Annotation Date                   :: 03/11/2024 12:51:32
            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)                     :: 4,357
            CDSs (total)                      :: 4,252
            Genes (coding)                    :: 4,182
            CDSs (with protein)               :: 4,182
            Genes (RNA)                       :: 105
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 79
            ncRNAs                            :: 4
            Pseudo Genes (total)              :: 70
            CDSs (without protein)            :: 70
            Pseudo Genes (ambiguous residues) :: 0 of 70
            Pseudo Genes (frameshifted)       :: 23 of 70
            Pseudo Genes (incomplete)         :: 57 of 70
            Pseudo Genes (internal stop)      :: 19 of 70
            Pseudo Genes (multiple problems)  :: 21 of 70
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP123254.1.
            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="YZLc5-3"
                     /isolation_source="feces"
                     /host="chicken"
                     /db_xref="taxon:587"
                     /plasmid="pYZLc5-3_2k"
                     /geo_loc_name="China:Yangzhou"
                     /collection_date="2019-04-01"
     gene            580..1224
                     /locus_tag="N4838_RS21685"
                     /old_locus_tag="N4838_021765"
     CDS             580..1224
                     /locus_tag="N4838_RS21685"
                     /old_locus_tag="N4838_021765"
                     /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"
     gene            1862..2302
                     /locus_tag="N4838_RS21690"
                     /old_locus_tag="N4838_021770"
     CDS             1862..2302
                     /locus_tag="N4838_RS21690"
                     /old_locus_tag="N4838_021770"
                     /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"
     ARG             581..1221
                     /name="qnrD1"
                     /gene="qnrD1"
                     /gene_name="quinolone resistance pentapeptide repeat
                     protein QnrD1"
                     /tool="amrfinderplus"
                     /drug_class="QUINOLONE"
                     /identity="100.0"
                     /coverage="100.0"
     Typing          331..486
                     /name="Col3M"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="98.089"
                     /coverage="100.0"
                     /evalue="2.29e-71"
ORIGIN
        1 aagcccgtca aactcactgc gttcgtctga ccaccccctt ttttcgcccc tgtatttggt
       61 cgctcaaaaa tgtggtggtc agacgcttcg cttgacgggg ggctttgccc ccaaaacgaa
      121 acacgttcac tggggttcac ttgccatcgc tggggcgtgt catttcgttt cggctccccc
      181 tgtttttccc tttcttcgct ggacgctcat caggataaaa acaaaaagcc taccgccctc
      241 gttttactcg gttggtcaaa tcgcttcttg ccacaaaaca agtttgtgac tttcagcgat
      301 ttcgcatcgt tttacttgtc agtttgcacg atgttaaaaa cgcactcaga agcccgcaaa
      361 accgttctaa actttcagcg tagatttggg tgttttatag ggtgatcgtg tcttaaaatc
      421 gtttcgaggg gctttaatgg ggatgaacgg gaggtttttg ctaactaact cgcccgttta
      481 acataaaagg gattgtatga atcaatttta gctagagttt aaggttgttc aaattaatgt
      541 acaatgattg cactgtataa ataaccaggt gtagcatgta tggaaaagca ctttatcaat
      601 gaaaagtttt cacgagatca atttacgggg aatagagtta aaaatattgc cttttcaaat
      661 tgtgattttt caggggttga tttaactgat actgaatttg ttgattgtag tttttacgac
      721 aggaatagct tggaagggtg tgattttaat agagccaaac taaaaaacgc tagctttaaa
      781 agctgcgatt tatcaatgag taattttaaa aacattagcg ccttaggtct tgaaattagt
      841 gagtgtttag ctcaaggagc tgattttcga ggggctaatt ttatgaatat gataactaca
      901 aggtcatggt tttgtagtgc ttatataacc aagacaaatc ttagttacgc taatttttct
      961 agagtcatat tagaaaagtg cgaactgtgg gaaaatcgct ggaatggcac tgtgataact
     1021 ggcgccgtgt ttcgtggctc cgatctttct tgtggggagt tttcatcgtt tgattggtct
     1081 ttggctgatt ttactggttg tgatttaacg ggtggggcgc ttggcgagct tgatgcaagg
     1141 cgaattaatt tagatggagt gaagttggat ggagagcagg cgcttcagct tgttgagagt
     1201 ttaggtgtta ttgttcaccg ataaaatcta ggtaaaaaac gcctaatgcc ccaatgtggt
     1261 actaatcaaa acggagcgaa gcgacatctt catcttgtct ttgcttttct ccatgatcag
     1321 ttattgggtc atggtctctt agctcgttaa tctggctaag tttggttagg ttgggcttct
     1381 ttcgacactt cgcaatccaa gaaatcccta gtccgttgat tggtgctctt atcaggtacg
     1441 cactgtaatc tttcgatacc gcagcgtgat tcggaggtag agccggaatt tcgttttccg
     1501 gtacgtttta ctaccacaat ttgcctgttt atcctttcgg agaccgggct aagtccgagt
     1561 caatcaagtg gtgcatttgg gttaatgtcg ttggctggta tttaatgaga acgtgacaag
     1621 cgcctctcac gttgctaaga ttggattgcg acgtctaatc tgagcaacga atgcacaaga
     1681 tttagagtac cagagccctg tgatgctgtc acggggcttt gttacatctg gagcttggta
     1741 aacctcataa attcaattcg caacgctcgc cgcaaggcgt gaacttgttt cacgtcgagg
     1801 aagcggaatt tctcgaaagc cttatactgt ctccgttcac acatgatcgg agggtgtctc
     1861 tatgtctcaa ttatttcgtt tggcatcgcc agaagattac gaatacatcg aagaattaaa
     1921 tttatgggaa ttgtcatttg ataagcgacc ggttcaaggg gttcgttgtg aagatccggt
     1981 gatcggggca gaaaaatata atcaagggcg tgaaaaattt aaggcgttag cgtcacggca
     2041 taaaaaacac tggaaaccga acggattgac cttttcggag ttgatccgct gggcaataga
     2101 atgcggaact ccagaacaat gtcagcttgt tttagcgtta taccattgca caaacgatga
     2161 tgattatcag gcgatgggaa ttcagttaag ccgaagtatt gataatgcaa atgtcagtcc
     2221 gatcatcttt ttcacaggta aaaatcaacg gttattaggt gatatttcga tgctaaaaca
     2281 gctcgaagaa aaggtgcgct gacgttaggt ttacctatta ttttatgtat tatcctatct
     2341 attattctat ctcttatttt atctatttcg tctgtaatag gtagaataat acatagaata
     2401 agatacagaa taatagatag acacaagatg acgttgtgtt atttcttacc cattaatcca
     2461 cctgttattc tacctattac tttacccgtt attgcaccca atttaggtat aacgggcaga
     2521 ataacgggtg aaataatggg tagaatcata gttttactaa cttgcacccc atgatacttt
     2581 cagtatcaat gccactcatt ttctggacga aaatgaatga cataaggctc cgccctctgg
     2641 ctattttctt cggctggacg cctgcgaaaa aaaccattca ccc
//
