LOCUS       NZ_CP120547             2683 bp    DNA     circular CON 20-OCT-2023
DEFINITION  Providencia sp. PROV024 plasmid pPROV024-qnrD1, complete sequence.
ACCESSION   NZ_CP120547
VERSION     NZ_CP120547.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN33763527
            Assembly: GCF_032709665.1
KEYWORDS    RefSeq.
SOURCE      Providencia sp. PROV024
  ORGANISM  Providencia sp. PROV024
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Morganellaceae; Providencia.
REFERENCE   1  (bases 1 to 2683)
  AUTHORS   Zhou,D.
  TITLE     Complete sequence of PROV024
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 2683)
  AUTHORS   Zhou,D.
  TITLE     Direct Submission
  JOURNAL   Submitted (15-MAR-2023) State Key Laboratory of Pathogen and
            Biosecurity, Beijing Institute of Microbiology and Epidemiology, No.
            20, Dongdajie, Fengtai, Beijing, Beijing 100071, China
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: HGAP v. v3.0
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 100.0x
            Sequencing Technology             :: PacBio RSII
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 10/18/2023 17:11:42
            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)                     :: 4,518
            CDSs (total)                      :: 4,414
            Genes (coding)                    :: 4,361
            CDSs (with protein)               :: 4,361
            Genes (RNA)                       :: 104
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 78
            ncRNAs                            :: 4
            Pseudo Genes (total)              :: 53
            CDSs (without protein)            :: 53
            Pseudo Genes (ambiguous residues) :: 0 of 53
            Pseudo Genes (frameshifted)       :: 22 of 53
            Pseudo Genes (incomplete)         :: 41 of 53
            Pseudo Genes (internal stop)      :: 13 of 53
            Pseudo Genes (multiple problems)  :: 16 of 53
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP120547.1.
            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 sp. PROV024"
                     /mol_type="genomic DNA"
                     /strain="PROV024"
                     /host="swine"
                     /db_xref="taxon:2949758"
                     /plasmid="pPROV024-qnrD1"
                     /geo_loc_name="China:Sichuan"
                     /collection_date="2017"
     gene            827..1471
                     /locus_tag="P3L56_RS22560"
                     /old_locus_tag="P3L56_22630"
     CDS             827..1471
                     /locus_tag="P3L56_RS22560"
                     /old_locus_tag="P3L56_22630"
                     /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            2109..2549
                     /locus_tag="P3L56_RS22565"
                     /old_locus_tag="P3L56_22635"
     CDS             2109..2549
                     /locus_tag="P3L56_RS22565"
                     /old_locus_tag="P3L56_22635"
                     /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             828..1468
                     /name="qnrD1"
                     /gene="qnrD1"
                     /gene_name="quinolone resistance pentapeptide repeat
                     protein QnrD1"
                     /tool="amrfinderplus"
                     /drug_class="QUINOLONE"
                     /identity="100.0"
                     /coverage="100.0"
     Typing          578..733
                     /name="Col3M"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="98.089"
                     /coverage="100.0"
                     /evalue="2.29e-71"
ORIGIN
        1 tgttatttct tacccattaa tccacctgtt attctaccta ttactttacc cgttattgca
       61 cccaatttag gtataacggg cagaataacg ggtgaaataa tgggtagaat catagtttta
      121 ctaacttgca ccccatgata ctttcagtat caatgccact cattttctgg acgaaaatga
      181 atgacataag gctccgccct ctggctattt tcttcggctg gacgcctgcg aaaaaaacca
      241 ttcacccaag cccgtcaaac tcactgcgtt cgtctgacca cccccttttt tcgcccctgt
      301 atttggtcgc tcaaaaatgt ggtggtcaga cgcttcgctt gacggggggc tttgccccca
      361 aaacgaaaca cgttcactgg ggttcacttg ccatcgctgg ggcgtgtcat ttcgtttcgg
      421 ctccccctgt ttttcccttt cttcgctgga cgctcatcag gataaaaaca aaaagcctac
      481 cgccctcgtt ttactcggtt ggtcaaatcg cttcttgcca caaaacaagt ttgtgacttt
      541 cagcgatttc gcatcgtttt acttgtcagt ttgcacgatg ttaaaaacgc actcagaagc
      601 ccgcaaaacc gttctaaact ttcagcgtag atttgggtgt tttatagggt gatcgtgtct
      661 taaaatcgtt tcgaggggct ttaatgggga tgaacgggag gtttttgcta actaactcgc
      721 ccgtttaaca taaaagggat tgtatgaatc aattttagct agagtttaag gttgttcaaa
      781 ttaatgtaca atgattgcac tgtataaata accaggtgta gcatgtatgg aaaagcactt
      841 tatcaatgaa aagttttcac gagatcaatt tacggggaat agagttaaaa atattgcctt
      901 ttcaaattgt gatttttcag gggttgattt aactgatact gaatttgttg attgtagttt
      961 ttacgacagg aatagcttgg aagggtgtga ttttaataga gccaaactaa aaaacgctag
     1021 ctttaaaagc tgcgatttat caatgagtaa ttttaaaaac attagcgcct taggtcttga
     1081 aattagtgag tgtttagctc aaggagctga ttttcgaggg gctaatttta tgaatatgat
     1141 aactacaagg tcatggtttt gtagtgctta tataaccaag acaaatctta gttacgctaa
     1201 tttttctaga gtcatattag aaaagtgcga actgtgggaa aatcgctgga atggcactgt
     1261 gataactggc gccgtgtttc gtggctccga tctttcttgt ggggagtttt catcgtttga
     1321 ttggtctttg gctgatttta ctggttgtga tttaacgggt ggggcgcttg gcgagcttga
     1381 tgcaaggcga attaatttag atggagtgaa gttggatgga gagcaggcgc ttcagcttgt
     1441 tgagagttta ggtgttattg ttcaccgata aaatctaggt aaaaaacgcc taatgcccca
     1501 atgtggtact aatcaaaacg gagcgaagcg acatcttcat cttgtctttg cttttctcca
     1561 tgatcagtta ttgggtcatg gtctcttagc tcgttaatct ggctaagttt ggttaggttg
     1621 ggcttctttc gacacttcgc aatccaagaa atccctagtc cgttgattgg tgctcttatc
     1681 aggtacgcac tgtaatcttt cgataccgca gcgtgattcg gaggtagagc cggaatttcg
     1741 ttttccggta cgttttacta ccacaatttg cctgtttatc ctttcggaga ccgggctaag
     1801 tccgagtcaa tcaagtggtg catttgggtt aatgtcgttg gctggtattt aatgagaacg
     1861 tgacaagcgc ctctcacgtt gctaagattg gattgcgacg tctaatctga gcaacgaatg
     1921 cacaagattt agagtaccag agccctgtga tgctgtcacg gggctttgtt acatctggag
     1981 cttggtaaac ctcataaatt caattcgcaa cgctcgccgc aaggcgtgaa cttgtttcac
     2041 gtcgaggaag cggaatttct cgaaagcctt atactgtctc cgttcacaca tgatcggagg
     2101 gtgtctctat gtctcaatta tttcgtttgg catcgccaga agattacgaa tacatcgaag
     2161 aattaaattt atgggaattg tcatttgata agcgaccggt tcaaggggtt cgttgtgaag
     2221 atccggtgat cggggcagaa aaatataatc aagggcgtga aaaatttaag gcgttagcgt
     2281 cacggcataa aaaacactgg aaaccgaacg gattgacctt ttcggagttg atccgctggg
     2341 caatagaatg cggaactcca gaacaatgtc agcttgtttt agcgttatac cattgcacaa
     2401 acgatgatga ttatcaggcg atgggaattc agttaagccg aagtattgat aatgcaaatg
     2461 tcagtccgat catctttttc acaggtaaaa atcaacggtt attaggtgat atttcgatgc
     2521 taaaacagct cgaagaaaag gtgcgctgac gttaggttta cctattattt tatgtattat
     2581 cctatctatt attctatctc ttattttatc tatttcgtct gtaataggta gaataataca
     2641 tagaataaga tacagaataa tagatagaca caagatgacg ttg
//
