LOCUS       NZ_CP135991             2683 bp    DNA     circular CON 03-MAR-2024
DEFINITION  Providencia zhijiangensis strain D4759 plasmid pD4759_2_1, complete
            sequence.
ACCESSION   NZ_CP135991
VERSION     NZ_CP135991.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN35719801
            Assembly: GCF_030315915.2
KEYWORDS    RefSeq.
SOURCE      Providencia zhijiangensis
  ORGANISM  Providencia zhijiangensis
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Morganellaceae; Providencia.
REFERENCE   1  (bases 1 to 2683)
  AUTHORS   Dong,X.
  TITLE     Genomic Revisitation and Reclassification of the Genus Providencia
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 2683)
  AUTHORS   Dong,X.
  TITLE     Direct Submission
  JOURNAL   Submitted (28-SEP-2023) State Key Laboratory for Diagnosis and
            Treatment of Infectious Diseases, National Clinical Research Center
            for Infectious Diseases, Collaborative Innovation Center for
            Diagnosis and Treatment of Infectious Diseases, The First Affiliated
            Hospital, Zhejiang University School of Medicine, huajiachi,
            Hangzhou, Zhejiang 310000, China
REFERENCE   3  (bases 1 to 2683)
  AUTHORS   Dong,X.
  TITLE     Direct Submission
  JOURNAL   Submitted (14-JUN-2023) State Key Laboratory for Diagnosis and
            Treatment of Infectious Diseases, National Clinical Research Center
            for Infectious Diseases, Collaborative Innovation Center for
            Diagnosis and Treatment of Infectious Diseases, The First Affiliated
            Hospital, Zhejiang University School of Medicine, huajiachi,
            Hangzhou, Zhejiang 310000, China
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method :: SPAdes v. 3.14.1; Unicycler v. 0.4.8
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 100.0x
            Sequencing Technology             :: Illumina HiSeq; Oxford Nanopore
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 03/03/2024 14:27:41
            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)                     :: 3,495
            CDSs (total)                      :: 3,390
            Genes (coding)                    :: 3,368
            CDSs (with protein)               :: 3,368
            Genes (RNA)                       :: 105
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 77
            ncRNAs                            :: 6
            Pseudo Genes (total)              :: 22
            CDSs (without protein)            :: 22
            Pseudo Genes (ambiguous residues) :: 0 of 22
            Pseudo Genes (frameshifted)       :: 7 of 22
            Pseudo Genes (incomplete)         :: 13 of 22
            Pseudo Genes (internal stop)      :: 8 of 22
            Pseudo Genes (multiple problems)  :: 5 of 22
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP135991.1.
            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 zhijiangensis"
                     /mol_type="genomic DNA"
                     /strain="D4759"
                     /isolation_source="bile"
                     /host="Homo sapiens"
                     /type_material="type strain of Providencia zhijiangensis"
                     /db_xref="taxon:3053982"
                     /plasmid="pD4759_2_1"
                     /geo_loc_name="China: Zhejiang"
                     /lat_lon="30.16 N 120.12 E"
                     /collection_date="2022"
                     /collected_by="Xu Dong"
     gene            complement(372..812)
                     /locus_tag="QS795_RS17460"
                     /old_locus_tag="QS795_017460"
     CDS             complement(372..812)
                     /locus_tag="QS795_RS17460"
                     /old_locus_tag="QS795_017460"
                     /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            complement(1450..2094)
                     /locus_tag="QS795_RS17465"
                     /old_locus_tag="QS795_017465"
     CDS             complement(1450..2094)
                     /locus_tag="QS795_RS17465"
                     /old_locus_tag="QS795_017465"
                     /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             complement(1454..2094)
                     /name="qnrD1"
                     /gene="qnrD1"
                     /gene_name="quinolone resistance pentapeptide repeat
                     protein QnrD1"
                     /tool="amrfinderplus"
                     /drug_class="QUINOLONE"
                     /identity="100.0"
                     /coverage="100.0"
     Typing          complement(2189..2344)
                     /name="Col3M"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="98.089"
                     /coverage="100.0"
                     /evalue="2.29e-71"
ORIGIN
        1 tttttttcgc aggcgtccag ccgaagaaaa tagccagagg gcggagcctt atgtcattca
       61 ttttcgtcca gaaaatgagt ggcattgata ctgaaagtat catggggtgc aagttagtaa
      121 aactatgatt ctacccatta tttcacccgt tattctgccc gttataccta aattgggtgc
      181 aataacgggt aaagtaatag gtagaataac aggtggatta atgggtaaga aataacacaa
      241 cgtcatcttg tgtctatcta ttattctgta tcttattcta tgtattattc tacctattac
      301 agacgaaata gataaaataa gagatagaat aatagatagg ataatacata aaataatagg
      361 taaacctaac gtcagcgcac cttttcttcg agctgtttta gcatcgaaat atcacctaat
      421 aaccgttgat ttttacctgt gaaaaagatg atcggactga catttgcatt atcaatactt
      481 cggcttaact gaattcccat cgcctgataa tcatcatcgt ttgtgcaatg gtataacgct
      541 aaaacaagct gacattgttc tggagttccg cattctattg cccagcggat caactccgaa
      601 aaggtcaatc cgttcggttt ccagtgtttt ttatgccgtg acgctaacgc cttaaatttt
      661 tcacgccctt gattatattt ttctgccccg atcaccggat cttcacaacg aaccccttga
      721 accggtcgct tatcaaatga caattcccat aaatttaatt cttcgatgta ttcgtaatct
      781 tctggcgatg ccaaacgaaa taattgagac atagagacac cctccgatca tgtgtgaacg
      841 gagacagtat aaggctttcg agaaattccg cttcctcgac gtgaaacaag ttcacgcctt
      901 gcggcgagcg ttgcgaattg aatttatgag gtttaccaag ctccagatgt aacaaagccc
      961 cgtgacagca tcacagggct ctggtactct aaatcttgtg cattcgttgc tcagattaga
     1021 cgtcgcaatc caatcttagc aacgtgagag gcgcttgtca cgttctcatt aaataccagc
     1081 caacgacatt aacccaaatg caccacttga ttgactcgga cttagcccgg tctccgaaag
     1141 gataaacagg caaattgtgg tagtaaaacg taccggaaaa cgaaattccg gctctacctc
     1201 cgaatcacgc tgcggtatcg aaagattaca gtgcgtacct gataagagca ccaatcaacg
     1261 gactagggat ttcttggatt gcgaagtgtc gaaagaagcc caacctaacc aaacttagcc
     1321 agattaacga gctaagagac catgacccaa taactgatca tggagaaaag caaagacaag
     1381 atgaagatgt cgcttcgctc cgttttgatt agtaccacat tggggcatta ggcgtttttt
     1441 acctagattt tatcggtgaa caataacacc taaactctca acaagctgaa gcgcctgctc
     1501 tccatccaac ttcactccat ctaaattaat tcgccttgca tcaagctcgc caagcgcccc
     1561 acccgttaaa tcacaaccag taaaatcagc caaagaccaa tcaaacgatg aaaactcccc
     1621 acaagaaaga tcggagccac gaaacacggc gccagttatc acagtgccat tccagcgatt
     1681 ttcccacagt tcgcactttt ctaatatgac tctagaaaaa ttagcgtaac taagatttgt
     1741 cttggttata taagcactac aaaaccatga ccttgtagtt atcatattca taaaattagc
     1801 ccctcgaaaa tcagctcctt gagctaaaca ctcactaatt tcaagaccta aggcgctaat
     1861 gtttttaaaa ttactcattg ataaatcgca gcttttaaag ctagcgtttt ttagtttggc
     1921 tctattaaaa tcacaccctt ccaagctatt cctgtcgtaa aaactacaat caacaaattc
     1981 agtatcagtt aaatcaaccc ctgaaaaatc acaatttgaa aaggcaatat ttttaactct
     2041 attccccgta aattgatctc gtgaaaactt ttcattgata aagtgctttt ccatacatgc
     2101 tacacctggt tatttataca gtgcaatcat tgtacattaa tttgaacaac cttaaactct
     2161 agctaaaatt gattcataca atccctttta tgttaaacgg gcgagttagt tagcaaaaac
     2221 ctcccgttca tccccattaa agcccctcga aacgatttta agacacgatc accctataaa
     2281 acacccaaat ctacgctgaa agtttagaac ggttttgcgg gcttctgagt gcgtttttaa
     2341 catcgtgcaa actgacaagt aaaacgatgc gaaatcgctg aaagtcacaa acttgttttg
     2401 tggcaagaag cgatttgacc aaccgagtaa aacgagggcg gtaggctttt tgtttttatc
     2461 ctgatgagcg tccagcgaag aaagggaaaa acagggggag ccgaaacgaa atgacacgcc
     2521 ccagcgatgg caagtgaacc ccagtgaacg tgtttcgttt tgggggcaaa gccccccgtc
     2581 aagcgaagcg tctgaccacc acatttttga gcgaccaaat acaggggcga aaaaaggggg
     2641 tggtcagacg aacgcagtga gtttgacggg cttgggtgaa tgg
//
