LOCUS       NZ_CP047351             2683 bp    DNA     circular CON 08-FEB-2024
DEFINITION  Proteus terrae subsp. cibarius strain ZN2 plasmid pZN2-qnrD,
            complete sequence.
ACCESSION   NZ_CP047351
VERSION     NZ_CP047351.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN13738053
            Assembly: GCF_011045835.1
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  JOURNAL   Unpublished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 Date                   :: 02/08/2024 03:11:48
            Annotation Pipeline :: NCBI Prokaryotic Genome Annotation Pipeline
            (PGAP)
            Annotation Method :: Best-placed reference protein set; GeneMarkS-2+
            Annotation Software revision      :: 6.6
            Features Annotated                :: Gene; CDS; rRNA; tRNA; ncRNA
            Genes (total)                     :: 3,801
            CDSs (total)                      :: 3,689
            Genes (coding)                    :: 3,653
            CDSs (with protein)               :: 3,653
            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)              :: 36
            CDSs (without protein)            :: 36
            Pseudo Genes (ambiguous residues) :: 0 of 36
            Pseudo Genes (frameshifted)       :: 9 of 36
            Pseudo Genes (incomplete)         :: 25 of 36
            Pseudo Genes (internal stop)      :: 6 of 36
            Pseudo Genes (multiple problems)  :: 4 of 36
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP047351.1.
            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="ZN2"
                     /isolation_source="a nose swab sample of swine origin"
                     /sub_species="cibarius"
                     /db_xref="taxon:626774"
                     /plasmid="pZN2-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            17..661
                     /locus_tag="GTH25_RS19090"
                     /old_locus_tag="GTH25_18930"
                     /db_xref="GeneID:57334992"
     CDS             17..661
                     /locus_tag="GTH25_RS19090"
                     /old_locus_tag="GTH25_18930"
                     /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"
                     /db_xref="GeneID:57334992"
                     /translation="MEKHFINEKFSRDQFTGNRVKNIAFSNCDFSGVDLTDTEFVDCSF
                     YDRNSLEGCDFNRAKLKNASFKSCDLSMSNFKNISALGLEISECLAQGADFRGANFMNM
                     ITTRSWFCSAYITKTNLSYANFSRVILEKCELWENRWNGTVITGAVFRGSDLSCGEFSS
                     FDWSLADFTGCDLTGGALGELDARRINLDGVKLDGEQALQLVESLGVIVHR"
                     /name="quinolone resistance pentapeptide repeat protein
                     QnrD1"
     gene            1299..1739
                     /locus_tag="GTH25_RS19095"
                     /old_locus_tag="GTH25_18935"
                     /db_xref="GeneID:57334993"
     CDS             1299..1739
                     /locus_tag="GTH25_RS19095"
                     /old_locus_tag="GTH25_18935"
                     /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"
                     /db_xref="GeneID:57334993"
                     /translation="MSQLFRLASPEDYEYIEELNLWELSFDKRPVQGVRCEDPVIGAEK
                     YNQGREKFKALASRHKKHWKPNGLTFSELIRWAIECGTPEQCQLVLALYHCTNDDDYQA
                     MGIQLSRSIDNANVSPIIFFTGKNQRLLGDISMLKQLEEKVR"
                     /name="hypothetical protein"
     ARG             18..658
                     /name="qnrD1"
                     /gene="qnrD1"
                     /gene_name="quinolone resistance pentapeptide repeat
                     protein QnrD1"
                     /tool="amrfinderplus"
                     /drug_class="QUINOLONE"
                     /identity="100.0"
                     /coverage="100.0"
     Typing          2451..2606
                     /name="Col3M"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="98.089"
                     /coverage="100.0"
                     /evalue="2.29e-71"
ORIGIN
        1 accaggtgta gcatgtatgg aaaagcactt tatcaatgaa aagttttcac gagatcaatt
       61 tacggggaat agagttaaaa atattgcctt ttcaaattgt gatttttcag gggttgattt
      121 aactgatact gaatttgttg attgtagttt ttacgacagg aatagcttgg aagggtgtga
      181 ttttaataga gccaaactaa aaaacgctag ctttaaaagc tgcgatttat caatgagtaa
      241 ttttaaaaac attagcgcct taggtcttga aattagtgag tgtttagctc aaggagctga
      301 ttttcgaggg gctaatttta tgaatatgat aactacaagg tcatggtttt gtagtgctta
      361 tataaccaag acaaatctta gttacgctaa tttttctaga gtcatattag aaaagtgcga
      421 actgtgggaa aatcgctgga atggcactgt gataactggc gccgtgtttc gtggctccga
      481 tctttcttgt ggggagtttt catcgtttga ttggtctttg gctgatttta ctggttgtga
      541 tttaacgggt ggggcgcttg gcgagcttga tgcaaggcga attaatttag atggagtgaa
      601 gttggatgga gagcaggcgc ttcagcttgt tgagagttta ggtgttattg ttcaccgata
      661 aaatctaggt aaaaaacgcc taatgcccca atgtggtact aatcaaaacg gagcgaagcg
      721 acatcttcat cttgtctttg cttttctcca tgatcagtta ttgggtcatg gtctcttagc
      781 tcgttaatct ggctaagttt ggttaggttg ggcttctttc gacacttcgc aatccaagaa
      841 atccctagtc cgttgattgg tgctcttatc aggtacgcac tgtaatcttt cgataccgca
      901 gcgtgattcg gaggtagagc cggaatttcg ttttccggta cgttttacta ccacaatttg
      961 cctgtttatc ctttcggaga ccgggctaag tccgagtcaa tcaagtggtg catttgggtt
     1021 aatgtcgttg gctggtattt aatgagaacg tgacaagcgc ctctcacgtt gctaagattg
     1081 gattgcgacg tctaatctga gcaacgaatg cacaagattt agagtaccag agccctgtga
     1141 tgctgtcacg gggctttgtt acatctggag cttggtaaac ctcataaatt caattcgcaa
     1201 cgctcgccgc aaggcgtgaa cttgtttcac gtcgaggaag cggaatttct cgaaagcctt
     1261 atactgtctc cgttcacaca tgatcggagg gtgtctctat gtctcaatta tttcgtttgg
     1321 catcgccaga agattacgaa tacatcgaag aattaaattt atgggaattg tcatttgata
     1381 agcgaccggt tcaaggggtt cgttgtgaag atccggtgat cggggcagaa aaatataatc
     1441 aagggcgtga aaaatttaag gcgttagcgt cacggcataa aaaacactgg aaaccgaacg
     1501 gattgacctt ttcggagttg atccgctggg caatagaatg cggaactcca gaacaatgtc
     1561 agcttgtttt agcgttatac cattgcacaa acgatgatga ttatcaggcg atgggaattc
     1621 agttaagccg aagtattgat aatgcaaatg tcagtccgat catctttttc acaggtaaaa
     1681 atcaacggtt attaggtgat atttcgatgc taaaacagct cgaagaaaag gtgcgctgac
     1741 gttaggttta cctattattt tatgtattat cctatctatt attctatctc ttattttatc
     1801 tatttcgtct gtaataggta gaataataca tagaataaga tacagaataa tagatagaca
     1861 caagatgacg ttgtgttatt tcttacccat taatccacct gttattctac ctattacttt
     1921 acccgttatt gcacccaatt taggtataac gggcagaata acgggtgaaa taatgggtag
     1981 aatcatagtt ttactaactt gcaccccatg atactttcag tatcaatgcc actcattttc
     2041 tggacgaaaa tgaatgacat aaggctccgc cctctggcta ttttcttcgg ctggacgcct
     2101 gcgaaaaaaa ccattcaccc aagcccgtca aactcactgc gttcgtctga ccaccccctt
     2161 ttttcgcccc tgtatttggt cgctcaaaaa tgtggtggtc agacgcttcg cttgacgggg
     2221 ggctttgccc ccaaaacgaa acacgttcac tggggttcac ttgccatcgc tggggcgtgt
     2281 catttcgttt cggctccccc tgtttttccc tttcttcgct ggacgctcat caggataaaa
     2341 acaaaaagcc taccgccctc gttttactcg gttggtcaaa tcgcttcttg ccacaaaaca
     2401 agtttgtgac tttcagcgat ttcgcatcgt tttacttgtc agtttgcacg atgttaaaaa
     2461 cgcactcaga agcccgcaaa accgttctaa actttcagcg tagatttggg tgttttatag
     2521 ggtgatcgtg tcttaaaatc gtttcgaggg gctttaatgg ggatgaacgg gaggtttttg
     2581 ctaactaact cgcccgttta acataaaagg gattgtatga atcaatttta gctagagttt
     2641 aaggttgttc aaattaatgt acaatgattg cactgtataa ata
//
