LOCUS       NZ_CP047641             2683 bp    DNA     circular CON 24-MAY-2024
DEFINITION  Proteus sp. ZN5 plasmid pZN5-qnrD, complete sequence.
ACCESSION   NZ_CP047641
VERSION     NZ_CP047641.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN13742196
            Assembly: GCF_011046025.1
KEYWORDS    RefSeq.
SOURCE      Proteus sp. ZN5
  ORGANISM  Proteus sp. ZN5
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Morganellaceae; Proteus.
REFERENCE   1  (bases 1 to 2683)
  AUTHORS   Peng,K.
  TITLE     The genomic epidemiology of tigecycline resistance gene tet(X)
            variants in a swine farm in China
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 2683)
  AUTHORS   Peng,K.
  TITLE     Direct Submission
  JOURNAL   Submitted (13-JAN-2020) College of Veterinary Medicine, Yangzhou
            University, No. 567, Wenchang Middle Road, Hanjiang District, Yangz,
            Yangzhou, Jiangsu 225000, China
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: Unicycler v. v0.4.4
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 50.0x
            Sequencing Technology :: Oxford Nanopore MiniION; Illumina HiSeq
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_011046025.1-RS_2024_05_24
            Annotation Date                   :: 05/24/2024 02:10:40
            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)                     :: 4,065
            CDSs (total)                      :: 3,950
            Genes (coding)                    :: 3,881
            CDSs (with protein)               :: 3,881
            Genes (RNA)                       :: 115
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 89
            ncRNAs                            :: 4
            Pseudo Genes (total)              :: 69
            CDSs (without protein)            :: 69
            Pseudo Genes (ambiguous residues) :: 0 of 69
            Pseudo Genes (frameshifted)       :: 24 of 69
            Pseudo Genes (incomplete)         :: 52 of 69
            Pseudo Genes (internal stop)      :: 8 of 69
            Pseudo Genes (multiple problems)  :: 13 of 69
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP047641.1.
            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="Proteus sp. ZN5"
                     /mol_type="genomic DNA"
                     /strain="ZN5"
                     /isolation_source="a nose swab sample of swine origin"
                     /db_xref="taxon:2697019"
                     /plasmid="pZN5-qnrD"
                     /geo_loc_name="China: Nantong, jiangsu province"
                     /lat_lon="31.41 N 120.11 E"
                     /collection_date="2018-05"
                     /collected_by="College of Veterinary Medicine, Yangzhou
                     University"
     gene            713..1357
                     /locus_tag="GTK47_RS20300"
                     /old_locus_tag="GTK47_20235"
     CDS             713..1357
                     /locus_tag="GTK47_RS20300"
                     /old_locus_tag="GTK47_20235"
                     /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            1995..2435
                     /locus_tag="GTK47_RS20305"
                     /old_locus_tag="GTK47_20240"
     CDS             1995..2435
                     /locus_tag="GTK47_RS20305"
                     /old_locus_tag="GTK47_20240"
                     /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             714..1354
                     /name="qnrD1"
                     /gene="qnrD1"
                     /gene_name="quinolone resistance pentapeptide repeat
                     protein QnrD1"
                     /tool="amrfinderplus"
                     /drug_class="QUINOLONE"
                     /identity="100.0"
                     /coverage="100.0"
     Typing          464..619
                     /name="Col3M"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="98.089"
                     /coverage="100.0"
                     /evalue="2.29e-71"
ORIGIN
        1 gttttactaa cttgcacccc atgatacttt cagtatcaat gccactcatt ttctggacga
       61 aaatgaatga cataaggctc cgccctctgg ctattttctt cggctggacg cctgcgaaaa
      121 aaaccattca cccaagcccg tcaaactcac tgcgttcgtc tgaccacccc cttttttcgc
      181 ccctgtattt ggtcgctcaa aaatgtggtg gtcagacgct tcgcttgacg gggggctttg
      241 cccccaaaac gaaacacgtt cactggggtt cacttgccat cgctggggcg tgtcatttcg
      301 tttcggctcc ccctgttttt ccctttcttc gctggacgct catcaggata aaaacaaaaa
      361 gcctaccgcc ctcgttttac tcggttggtc aaatcgcttc ttgccacaaa acaagtttgt
      421 gactttcagc gatttcgcat cgttttactt gtcagtttgc acgatgttaa aaacgcactc
      481 agaagcccgc aaaaccgttc taaactttca gcgtagattt gggtgtttta tagggtgatc
      541 gtgtcttaaa atcgtttcga ggggctttaa tggggatgaa cgggaggttt ttgctaacta
      601 actcgcccgt ttaacataaa agggattgta tgaatcaatt ttagctagag tttaaggttg
      661 ttcaaattaa tgtacaatga ttgcactgta taaataacca ggtgtagcat gtatggaaaa
      721 gcactttatc aatgaaaagt tttcacgaga tcaatttacg gggaatagag ttaaaaatat
      781 tgccttttca aattgtgatt tttcaggggt tgatttaact gatactgaat ttgttgattg
      841 tagtttttac gacaggaata gcttggaagg gtgtgatttt aatagagcca aactaaaaaa
      901 cgctagcttt aaaagctgcg atttatcaat gagtaatttt aaaaacatta gcgccttagg
      961 tcttgaaatt agtgagtgtt tagctcaagg agctgatttt cgaggggcta attttatgaa
     1021 tatgataact acaaggtcat ggttttgtag tgcttatata accaagacaa atcttagtta
     1081 cgctaatttt tctagagtca tattagaaaa gtgcgaactg tgggaaaatc gctggaatgg
     1141 cactgtgata actggcgccg tgtttcgtgg ctccgatctt tcttgtgggg agttttcatc
     1201 gtttgattgg tctttggctg attttactgg ttgtgattta acgggtgggg cgcttggcga
     1261 gcttgatgca aggcgaatta atttagatgg agtgaagttg gatggagagc aggcgcttca
     1321 gcttgttgag agtttaggtg ttattgttca ccgataaaat ctaggtaaaa aacgcctaat
     1381 gccccaatgt ggtactaatc aaaacggagc gaagcgacat cttcatcttg tctttgcttt
     1441 tctccatgat cagttattgg gtcatggtct cttagctcgt taatctggct aagtttggtt
     1501 aggttgggct tctttcgaca cttcgcaatc caagaaatcc ctagtccgtt gattggtgct
     1561 cttatcaggt acgcactgta atctttcgat accgcagcgt gattcggagg tagagccgga
     1621 atttcgtttt ccggtacgtt ttactaccac aatttgcctg tttatccttt cggagaccgg
     1681 gctaagtccg agtcaatcaa gtggtgcatt tgggttaatg tcgttggctg gtatttaatg
     1741 agaacgtgac aagcgcctct cacgttgcta agattggatt gcgacgtcta atctgagcaa
     1801 cgaatgcaca agatttagag taccagagcc ctgtgatgct gtcacggggc tttgttacat
     1861 ctggagcttg gtaaacctca taaattcaat tcgcaacgct cgccgcaagg cgtgaacttg
     1921 tttcacgtcg aggaagcgga atttctcgaa agccttatac tgtctccgtt cacacatgat
     1981 cggagggtgt ctctatgtct caattatttc gtttggcatc gccagaagat tacgaataca
     2041 tcgaagaatt aaatttatgg gaattgtcat ttgataagcg accggttcaa ggggttcgtt
     2101 gtgaagatcc ggtgatcggg gcagaaaaat ataatcaagg gcgtgaaaaa tttaaggcgt
     2161 tagcgtcacg gcataaaaaa cactggaaac cgaacggatt gaccttttcg gagttgatcc
     2221 gctgggcaat agaatgcgga actccagaac aatgtcagct tgttttagcg ttataccatt
     2281 gcacaaacga tgatgattat caggcgatgg gaattcagtt aagccgaagt attgataatg
     2341 caaatgtcag tccgatcatc tttttcacag gtaaaaatca acggttatta ggtgatattt
     2401 cgatgctaaa acagctcgaa gaaaaggtgc gctgacgtta ggtttaccta ttattttatg
     2461 tattatccta tctattattc tatctcttat tttatctatt tcgtctgtaa taggtagaat
     2521 aatacataga ataagataca gaataataga tagacacaag atgacgttgt gttatttctt
     2581 acccattaat ccacctgtta ttctacctat tactttaccc gttattgcac ccaatttagg
     2641 tataacgggc agaataacgg gtgaaataat gggtagaatc ata
//
