LOCUS       NZ_CP047354             2683 bp    DNA     circular CON 07-APR-2024
DEFINITION  Proteus mirabilis strain ZA25 plasmid pZA25-qnrD, complete sequence.
ACCESSION   NZ_CP047354
VERSION     NZ_CP047354.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN13738061
            Assembly: GCF_011045855.1
KEYWORDS    RefSeq.
SOURCE      Proteus mirabilis
  ORGANISM  Proteus mirabilis
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Morganellaceae; Proteus.
REFERENCE   1  (bases 1 to 2683)
  AUTHORS   Peng,K. and Li,R.
  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  JOURNAL   Unpublished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. and Li,R.
  TITLE     Direct Submission
  JOURNAL   Submitted (05-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_011045855.1-RS_2024_04_07
            Annotation Date                   :: 04/07/2024 07:22:14
            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)                     :: 3,843
            CDSs (total)                      :: 3,734
            Genes (coding)                    :: 3,687
            CDSs (with protein)               :: 3,687
            Genes (RNA)                       :: 109
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 83
            ncRNAs                            :: 4
            Pseudo Genes (total)              :: 47
            CDSs (without protein)            :: 47
            Pseudo Genes (ambiguous residues) :: 0 of 47
            Pseudo Genes (frameshifted)       :: 13 of 47
            Pseudo Genes (incomplete)         :: 32 of 47
            Pseudo Genes (internal stop)      :: 10 of 47
            Pseudo Genes (multiple problems)  :: 7 of 47
            CRISPR Arrays                     :: 1
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP047354.1.
            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 mirabilis"
                     /mol_type="genomic DNA"
                     /strain="ZA25"
                     /isolation_source="a anal swab sample of swine origin"
                     /db_xref="taxon:584"
                     /plasmid="pZA25-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            620..1264
                     /locus_tag="GTH26_RS19335"
                     /old_locus_tag="GTH26_19220"
     CDS             620..1264
                     /locus_tag="GTH26_RS19335"
                     /old_locus_tag="GTH26_19220"
                     /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            1902..2342
                     /locus_tag="GTH26_RS19340"
                     /old_locus_tag="GTH26_19225"
     CDS             1902..2342
                     /locus_tag="GTH26_RS19340"
                     /old_locus_tag="GTH26_19225"
                     /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             621..1261
                     /name="qnrD1"
                     /gene="qnrD1"
                     /gene_name="quinolone resistance pentapeptide repeat
                     protein QnrD1"
                     /tool="amrfinderplus"
                     /drug_class="QUINOLONE"
                     /identity="100.0"
                     /coverage="100.0"
     Typing          371..526
                     /name="Col3M"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="98.089"
                     /coverage="100.0"
                     /evalue="2.29e-71"
ORIGIN
        1 ttttcttcgg ctggacgcct gcgaaaaaaa ccattcaccc aagcccgtca aactcactgc
       61 gttcgtctga ccaccccctt ttttcgcccc tgtatttggt cgctcaaaaa tgtggtggtc
      121 agacgcttcg cttgacgggg ggctttgccc ccaaaacgaa acacgttcac tggggttcac
      181 ttgccatcgc tggggcgtgt catttcgttt cggctccccc tgtttttccc tttcttcgct
      241 ggacgctcat caggataaaa acaaaaagcc taccgccctc gttttactcg gttggtcaaa
      301 tcgcttcttg ccacaaaaca agtttgtgac tttcagcgat ttcgcatcgt tttacttgtc
      361 agtttgcacg atgttaaaaa cgcactcaga agcccgcaaa accgttctaa actttcagcg
      421 tagatttggg tgttttatag ggtgatcgtg tcttaaaatc gtttcgaggg gctttaatgg
      481 ggatgaacgg gaggtttttg ctaactaact cgcccgttta acataaaagg gattgtatga
      541 atcaatttta gctagagttt aaggttgttc aaattaatgt acaatgattg cactgtataa
      601 ataaccaggt gtagcatgta tggaaaagca ctttatcaat gaaaagtttt cacgagatca
      661 atttacgggg aatagagtta aaaatattgc cttttcaaat tgtgattttt caggggttga
      721 tttaactgat actgaatttg ttgattgtag tttttacgac aggaatagct tggaagggtg
      781 tgattttaat agagccaaac taaaaaacgc tagctttaaa agctgcgatt tatcaatgag
      841 taattttaaa aacattagcg ccttaggtct tgaaattagt gagtgtttag ctcaaggagc
      901 tgattttcga ggggctaatt ttatgaatat gataactaca aggtcatggt tttgtagtgc
      961 ttatataacc aagacaaatc ttagttacgc taatttttct agagtcatat tagaaaagtg
     1021 cgaactgtgg gaaaatcgct ggaatggcac tgtgataact ggcgccgtgt ttcgtggctc
     1081 cgatctttct tgtggggagt tttcatcgtt tgattggtct ttggctgatt ttactggttg
     1141 tgatttaacg ggtggggcgc ttggcgagct tgatgcaagg cgaattaatt tagatggagt
     1201 gaagttggat ggagagcagg cgcttcagct tgttgagagt ttaggtgtta ttgttcaccg
     1261 ataaaatcta ggtaaaaaac gcctaatgcc ccaatgtggt actaatcaaa acggagcgaa
     1321 gcgacatctt catcttgtct ttgcttttct ccatgatcag ttattgggtc atggtctctt
     1381 agctcgttaa tctggctaag tttggttagg ttgggcttct ttcgacactt cgcaatccaa
     1441 gaaatcccta gtccgttgat tggtgctctt atcaggtacg cactgtaatc tttcgatacc
     1501 gcagcgtgat tcggaggtag agccggaatt tcgttttccg gtacgtttta ctaccacaat
     1561 ttgcctgttt atcctttcgg agaccgggct aagtccgagt caatcaagtg gtgcatttgg
     1621 gttaatgtcg ttggctggta tttaatgaga acgtgacaag cgcctctcac gttgctaaga
     1681 ttggattgcg acgtctaatc tgagcaacga atgcacaaga tttagagtac cagagccctg
     1741 tgatgctgtc acggggcttt gttacatctg gagcttggta aacctcataa attcaattcg
     1801 caacgctcgc cgcaaggcgt gaacttgttt cacgtcgagg aagcggaatt tctcgaaagc
     1861 cttatactgt ctccgttcac acatgatcgg agggtgtctc tatgtctcaa ttatttcgtt
     1921 tggcatcgcc agaagattac gaatacatcg aagaattaaa tttatgggaa ttgtcatttg
     1981 ataagcgacc ggttcaaggg gttcgttgtg aagatccggt gatcggggca gaaaaatata
     2041 atcaagggcg tgaaaaattt aaggcgttag cgtcacggca taaaaaacac tggaaaccga
     2101 acggattgac cttttcggag ttgatccgct gggcaataga atgcggaact ccagaacaat
     2161 gtcagcttgt tttagcgtta taccattgca caaacgatga tgattatcag gcgatgggaa
     2221 ttcagttaag ccgaagtatt gataatgcaa atgtcagtcc gatcatcttt ttcacaggta
     2281 aaaatcaacg gttattaggt gatatttcga tgctaaaaca gctcgaagaa aaggtgcgct
     2341 gacgttaggt ttacctatta ttttatgtat tatcctatct attattctat ctcttatttt
     2401 atctatttcg tctgtaatag gtagaataat acatagaata agatacagaa taatagatag
     2461 acacaagatg acgttgtgtt atttcttacc cattaatcca cctgttattc tacctattac
     2521 tttacccgtt attgcaccca atttaggtat aacgggcaga ataacgggtg aaataatggg
     2581 tagaatcata gttttactaa cttgcacccc atgatacttt cagtatcaat gccactcatt
     2641 ttctggacga aaatgaatga cataaggctc cgccctctgg cta
//
