LOCUS       NZ_CP045539             2655 bp    DNA     circular CON 07-APR-2024
DEFINITION  Proteus mirabilis strain CRE14IB plasmid pIB_COL3M, complete
            sequence.
ACCESSION   NZ_CP045539
VERSION     NZ_CP045539.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN13082492
            Assembly: GCF_009429045.2
KEYWORDS    RefSeq.
SOURCE      Proteus mirabilis
  ORGANISM  Proteus mirabilis
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Morganellaceae; Proteus.
REFERENCE   1  (bases 1 to 2655)
  AUTHORS   Bitar,I., Mattioni Marchetti,V., Mercato,A., Nucleo,E., Anesi,A.,
            Bracco,S., Rognoni,V., Hrabak,J. and Migliavacca,R.
  TITLE     Complete Genome and Plasmids Sequences of a Clinical Proteus
            mirabilis Isolate Producing Plasmid Mediated NDM-1 from Italy
  JOURNAL   Microorganisms 8 (3), 339 (2020)
   PUBMED   32121207
  REMARK    Publication Status: Online-Only
REFERENCE   2  (bases 1 to 2655)
  AUTHORS   Bitar,I.
  TITLE     Direct Submission
  JOURNAL   Submitted (22-OCT-2019) Microbiology, Charles University in Prague,
            Alej Svobody 1655/76, Plzen 1 32300, Czech Republic
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: HGAP v. 4
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 152.0x
            Sequencing Technology             :: PacBio Sequel
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_009429045.2-RS_2024_04_07
            Annotation Date                   :: 04/07/2024 06:58:12
            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)                     :: 3,856
            CDSs (total)                      :: 3,747
            Genes (coding)                    :: 3,675
            CDSs (with protein)               :: 3,675
            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)              :: 72
            CDSs (without protein)            :: 72
            Pseudo Genes (ambiguous residues) :: 0 of 72
            Pseudo Genes (frameshifted)       :: 25 of 72
            Pseudo Genes (incomplete)         :: 46 of 72
            Pseudo Genes (internal stop)      :: 15 of 72
            Pseudo Genes (multiple problems)  :: 11 of 72
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP045539.1.
            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..2655
                     /organism="Proteus mirabilis"
                     /mol_type="genomic DNA"
                     /strain="CRE14IB"
                     /isolation_source="urine catheter"
                     /host="Homo sapiens"
                     /db_xref="taxon:584"
                     /plasmid="pIB_COL3M"
                     /geo_loc_name="Italy: Lodi"
                     /lat_lon="45.30 N 9.50 E"
                     /collection_date="2019-04-03"
                     /collected_by="S. Angelo Lodigiano hospital"
     gene            complement(join(2026..2655,1..6))
                     /locus_tag="GD587_RS18600"
                     /old_locus_tag="GD587_18740"
     CDS             complement(join(2026..2655,1..6))
                     /locus_tag="GD587_RS18600"
                     /old_locus_tag="GD587_18740"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_006663235.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="QnrD family quinolone resistance pentapeptide
                     repeat protein"
                     /protein_id="WP_152964648.1"
                     /translation="MTINEKFSRDQFTGNRVKNIAFSNCDFSGVDLTDTEFVDCSFYDR
                     NSLEGCDFNRAKLKNASFKSCDLSMSNFKNISALGLEISECLAQGADFRGANFMNMITT
                     RSWFCSAYITKTNLSYANFSRVILEKCELWENRWNGTVITGAVFRGSDLSCGEFSSFDW
                     SLADFTGCDLTGGALGELDARRINLDGVKLDGEQALQLVESLGVIVHR"
                     /name="QnrD family quinolone resistance pentapeptide repeat
                     protein"
     gene            complement(948..1388)
                     /locus_tag="GD587_RS18605"
                     /old_locus_tag="GD587_18745"
     CDS             complement(948..1388)
                     /locus_tag="GD587_RS18605"
                     /old_locus_tag="GD587_18745"
                     /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             complement(2030..2655)
                     /name="qnrD"
                     /gene="qnrD"
                     /gene_name="QnrD family quinolone resistance pentapeptide
                     repeat protein"
                     /tool="amrfinderplus"
                     /drug_class="QUINOLONE"
                     /identity="100.0"
                     /coverage="97.66"
     ARG             complement(2027..2655)
                     /name="QnrD1"
                     /gene="QnrD1"
                     /gene_name="quinolone resistance protein (qnr)"
                     /tool="rgi"
                     /drug_class="fluoroquinolone antibiotic"
                     /identity="100.0"
                     /coverage="97.66"
     Typing          complement(82..237)
                     /name="Col3M"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="98.089"
                     /coverage="100.0"
                     /evalue="2.29e-71"
ORIGIN
        1 ggttatttat acagtgcaat cattgtacat taatttgaac aaccttaaac tctagctaaa
       61 attgattcat acaatccctt ttatgttaaa cgggcgagtt agttagcaaa aacctcccgt
      121 tcatccccat taaagcccct cgaaacgatt ttaagacacg atcaccctat aaaacaccca
      181 aatctacgct gaaagtttag aacggttttg cgggcttctg agtgcgtttt taacatcgtg
      241 caaactgaca agtaaaacga tgcgaaatcg ctgaaagtca caaacttgtt ttgtggcaag
      301 aagcgatttg accaaccgag taaaacgagg gcggtaggct ttttgttttt atcctgatga
      361 gcgtccagcg aagaaaggga aaaacagggg gagccgaaac gaaatgacac gccccagcga
      421 tggcaagtga accccagtga acgtgtttcg ttttgggggc aaagcccccc gtcaagcgaa
      481 gcgtctgacc accacatttt tgagcgacca aatacagggg cgaaaaaagg gggtggtcag
      541 acgaacgcag tgagtttgac gggcttgggt gaatggtttt tttcgcaggc gtccagccga
      601 agaaaatagc cagagggcgg agccttatgt cattcatttt cgtccagaaa atgagtggca
      661 ttgatactga aagtatcatg gggtgcaagt tagtaaaact atgattctac ccattatttc
      721 acccgttatt ctgcccgtta tacctaaatt gggtgcaata acgggtaaag taataggtag
      781 aataacaggt ggattaatgg gtaagaaata acacaacgtc atcttgtgtc tatctattat
      841 tctgtatctt attctatgta ttattctacc tattacagac gaaatagata aaataagaga
      901 tagaataata gataggataa tacataaaat aataggtaaa cctaacgtca gcgcaccttt
      961 tcttcgagct gttttagcat cgaaatatca cctaataacc gttgattttt acctgtgaaa
     1021 aagatgatcg gactgacatt tgcattatca atacttcggc ttaactgaat tcccatcgcc
     1081 tgataatcat catcgtttgt gcaatggtat aacgctaaaa caagctgaca ttgttctgga
     1141 gttccgcatt ctattgccca gcggatcaac tccgaaaagg tcaatccgtt cggtttccag
     1201 tgttttttat gccgtgacgc taacgcctta aatttttcac gcccttgatt atatttttct
     1261 gccccgatca ccggatcttc acaacgaacc ccttgaaccg gtcgcttatc aaatgacaat
     1321 tcccataaat ttaattcttc gatgtattcg taatcttctg gcgatgccaa acgaaataat
     1381 tgagacatag agacaccctc cgatcatgtg tgaacggaga cagtataagg ctttcgagaa
     1441 attccgcttc ctcgacgtga aacaagttca cgccttgcgg cgagcgttgc gaattgaatt
     1501 tatgaggttt accaagctcc agatgtaaca aagccccgtg acagcatcac agggctctgg
     1561 tactctaaat cttgtgcatt cgttgctcag attagacgtc gcaatccaat cttagcaacg
     1621 tgagaggcgc ttgtcacgtt ctcattaaat accagccaac gacattaacc caaatgcacc
     1681 acttgattga ctcggactta gcccggtctc cgaaaggata aacaggcaaa ttgtggtagt
     1741 aaaacgtacc ggaaaacgaa attccggctc tacctccgaa tcacgctgcg gtatcgaaag
     1801 attacagtgc gtacctgata agagcaccaa tcaacggact agggatttct tggattgcga
     1861 agtgtcgaaa gaagcccaac ctaaccaaac ttagccagat taacgagcta agagaccatg
     1921 acccaataac tgatcatgga gaaaagcaaa gacaagatga agatgtcgct tcgctccgtt
     1981 ttgattagta ccacattggg gcattaggcg ttttttacct agattttatc ggtgaacaat
     2041 aacacctaaa ctctcaacaa gctgaagcgc ctgctctcca tccaacttca ctccatctaa
     2101 attaattcgc cttgcatcaa gctcgccaag cgccccaccc gttaaatcac aaccagtaaa
     2161 atcagccaaa gaccaatcaa acgatgaaaa ctccccacaa gaaagatcgg agccacgaaa
     2221 cacggcgcca gttatcacag tgccattcca gcgattttcc cacagttcgc acttttctaa
     2281 tatgactcta gaaaaattag cgtaactaag atttgtcttg gttatataag cactacaaaa
     2341 ccatgacctt gtagttatca tattcataaa attagcccct cgaaaatcag ctccttgagc
     2401 taaacactca ctaatttcaa gacctaaggc gctaatgttt ttaaaattac tcattgataa
     2461 atcgcagctt ttaaagctag cgttttttag tttggctcta ttaaaatcac acccttccaa
     2521 gctattcctg tcgtaaaaac tacaatcaac aaattcagta tcagttaaat caacccctga
     2581 aaaatcacaa tttgaaaagg caatattttt aactctattc cccgtaaatt gatctcgtga
     2641 aaacttttca ttgat
//
