LOCUS       NZ_CP047343             2683 bp    DNA     circular CON 01-APR-2024
DEFINITION  Proteus terrae subsp. cibarius strain ZF1 plasmid pZF1-qnrD,
            complete sequence.
ACCESSION   NZ_CP047343
VERSION     NZ_CP047343.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN13738032
            Assembly: GCF_011045795.1
KEYWORDS    RefSeq.
SOURCE      Proteus terrae subsp. cibarius
  ORGANISM  Proteus terrae subsp. cibarius
            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  JOURNAL   Unpublished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_011045795.1-RS_2024_04_01
            Annotation Date                   :: 04/01/2024 03:57:49
            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)                     :: 4,042
            CDSs (total)                      :: 3,930
            Genes (coding)                    :: 3,881
            CDSs (with protein)               :: 3,881
            Genes (RNA)                       :: 112
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 86
            ncRNAs                            :: 4
            Pseudo Genes (total)              :: 49
            CDSs (without protein)            :: 49
            Pseudo Genes (ambiguous residues) :: 0 of 49
            Pseudo Genes (frameshifted)       :: 17 of 49
            Pseudo Genes (incomplete)         :: 29 of 49
            Pseudo Genes (internal stop)      :: 10 of 49
            Pseudo Genes (multiple problems)  :: 6 of 49
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP047343.1.
            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 terrae subsp. cibarius"
                     /mol_type="genomic DNA"
                     /strain="ZF1"
                     /isolation_source="a feces sample of swine origin"
                     /sub_species="cibarius"
                     /db_xref="taxon:626774"
                     /plasmid="pZF1-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            533..973
                     /locus_tag="GTH23_RS20290"
                     /old_locus_tag="GTH23_20215"
     CDS             533..973
                     /locus_tag="GTH23_RS20290"
                     /old_locus_tag="GTH23_20215"
                     /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            1934..2578
                     /locus_tag="GTH23_RS20295"
                     /old_locus_tag="GTH23_20220"
     CDS             1934..2578
                     /locus_tag="GTH23_RS20295"
                     /old_locus_tag="GTH23_20220"
                     /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             1935..2575
                     /name="qnrD1"
                     /gene="qnrD1"
                     /gene_name="quinolone resistance pentapeptide repeat
                     protein QnrD1"
                     /tool="amrfinderplus"
                     /drug_class="QUINOLONE"
                     /identity="100.0"
                     /coverage="100.0"
     Typing          1685..1840
                     /name="Col3M"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="98.089"
                     /coverage="100.0"
                     /evalue="2.29e-71"
ORIGIN
        1 catggtctct tagctcgtta atctggctaa gtttggttag gttgggcttc tttcgacact
       61 tcgcaatcca agaaatccct agtccgttga ttggtgctct tatcaggtac gcactgtaat
      121 ctttcgatac cgcagcgtga ttcggaggta gagccggaat ttcgttttcc ggtacgtttt
      181 actaccacaa tttgcctgtt tatcctttcg gagaccgggc taagtccgag tcaatcaagt
      241 ggtgcatttg ggttaatgtc gttggctggt atttaatgag aacgtgacaa gcgcctctca
      301 cgttgctaag attggattgc gacgtctaat ctgagcaacg aatgcacaag atttagagta
      361 ccagagccct gtgatgctgt cacggggctt tgttacatct ggagcttggt aaacctcata
      421 aattcaattc gcaacgctcg ccgcaaggcg tgaacttgtt tcacgtcgag gaagcggaat
      481 ttctcgaaag ccttatactg tctccgttca cacatgatcg gagggtgtct ctatgtctca
      541 attatttcgt ttggcatcgc cagaagatta cgaatacatc gaagaattaa atttatggga
      601 attgtcattt gataagcgac cggttcaagg ggttcgttgt gaagatccgg tgatcggggc
      661 agaaaaatat aatcaagggc gtgaaaaatt taaggcgtta gcgtcacggc ataaaaaaca
      721 ctggaaaccg aacggattga ccttttcgga gttgatccgc tgggcaatag aatgcggaac
      781 tccagaacaa tgtcagcttg ttttagcgtt ataccattgc acaaacgatg atgattatca
      841 ggcgatggga attcagttaa gccgaagtat tgataatgca aatgtcagtc cgatcatctt
      901 tttcacaggt aaaaatcaac ggttattagg tgatatttcg atgctaaaac agctcgaaga
      961 aaaggtgcgc tgacgttagg tttacctatt attttatgta ttatcctatc tattattcta
     1021 tctcttattt tatctatttc gtctgtaata ggtagaataa tacatagaat aagatacaga
     1081 ataatagata gacacaagat gacgttgtgt tatttcttac ccattaatcc acctgttatt
     1141 ctacctatta ctttacccgt tattgcaccc aatttaggta taacgggcag aataacgggt
     1201 gaaataatgg gtagaatcat agttttacta acttgcaccc catgatactt tcagtatcaa
     1261 tgccactcat tttctggacg aaaatgaatg acataaggct ccgccctctg gctattttct
     1321 tcggctggac gcctgcgaaa aaaaccattc acccaagccc gtcaaactca ctgcgttcgt
     1381 ctgaccaccc ccttttttcg cccctgtatt tggtcgctca aaaatgtggt ggtcagacgc
     1441 ttcgcttgac ggggggcttt gcccccaaaa cgaaacacgt tcactggggt tcacttgcca
     1501 tcgctggggc gtgtcatttc gtttcggctc cccctgtttt tccctttctt cgctggacgc
     1561 tcatcaggat aaaaacaaaa agcctaccgc cctcgtttta ctcggttggt caaatcgctt
     1621 cttgccacaa aacaagtttg tgactttcag cgatttcgca tcgttttact tgtcagtttg
     1681 cacgatgtta aaaacgcact cagaagcccg caaaaccgtt ctaaactttc agcgtagatt
     1741 tgggtgtttt atagggtgat cgtgtcttaa aatcgtttcg aggggcttta atggggatga
     1801 acgggaggtt tttgctaact aactcgcccg tttaacataa aagggattgt atgaatcaat
     1861 tttagctaga gtttaaggtt gttcaaatta atgtacaatg attgcactgt ataaataacc
     1921 aggtgtagca tgtatggaaa agcactttat caatgaaaag ttttcacgag atcaatttac
     1981 ggggaataga gttaaaaata ttgccttttc aaattgtgat ttttcagggg ttgatttaac
     2041 tgatactgaa tttgttgatt gtagttttta cgacaggaat agcttggaag ggtgtgattt
     2101 taatagagcc aaactaaaaa acgctagctt taaaagctgc gatttatcaa tgagtaattt
     2161 taaaaacatt agcgccttag gtcttgaaat tagtgagtgt ttagctcaag gagctgattt
     2221 tcgaggggct aattttatga atatgataac tacaaggtca tggttttgta gtgcttatat
     2281 aaccaagaca aatcttagtt acgctaattt ttctagagtc atattagaaa agtgcgaact
     2341 gtgggaaaat cgctggaatg gcactgtgat aactggcgcc gtgtttcgtg gctccgatct
     2401 ttcttgtggg gagttttcat cgtttgattg gtctttggct gattttactg gttgtgattt
     2461 aacgggtggg gcgcttggcg agcttgatgc aaggcgaatt aatttagatg gagtgaagtt
     2521 ggatggagag caggcgcttc agcttgttga gagtttaggt gttattgttc accgataaaa
     2581 tctaggtaaa aaacgcctaa tgccccaatg tggtactaat caaaacggag cgaagcgaca
     2641 tcttcatctt gtctttgctt ttctccatga tcagttattg ggt
//
