LOCUS       NZ_CP087628             1856 bp    DNA     linear   CON 08-JUN-2024
DEFINITION  Klebsiella pneumoniae subsp. pneumoniae strain DD02280 plasmid
            pDD02280-5.
ACCESSION   NZ_CP087628
VERSION     NZ_CP087628.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN22822726
            Assembly: GCF_023066665.1
KEYWORDS    RefSeq.
SOURCE      Klebsiella pneumoniae subsp. pneumoniae
  ORGANISM  Klebsiella pneumoniae subsp. pneumoniae
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Klebsiella/Raoultella group; Klebsiella.
REFERENCE   1  (bases 1 to 1856)
  AUTHORS   Jiang,J., Su,J., Xu,X. and Wang,M.
  TITLE     Insertion sequence medicated mrgB disruption is the major mechanism
            of polymyxin resistance in carbapenem-resistant Klebsiella
            pneumoniae isolates from China
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 1856)
  AUTHORS   Jiang,J., Su,J., Xu,X. and Wang,M.
  TITLE     Direct Submission
  JOURNAL   Submitted (03-NOV-2021) Institute of Antibiotics, Institute of
            Antibiotics, No. 12 Wulumuqi Road, Shanghai, Shanghai 200000, China
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Date                     :: 01-AUG-2021
            Assembly Method                   :: Unicycler v. v0.4.9
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 200x
            Sequencing Technology :: Illumina+Oxford Nanopore GridION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_023066665.1-RS_2024_06_08
            Annotation Date                   :: 06/08/2024 03:58:05
            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)                     :: 5,950
            CDSs (total)                      :: 5,828
            Genes (coding)                    :: 5,640
            CDSs (with protein)               :: 5,640
            Genes (RNA)                       :: 122
            rRNAs                             :: 9, 8, 8 (5S, 16S, 23S)
            complete rRNAs                    :: 9, 8, 8 (5S, 16S, 23S)
            tRNAs                             :: 85
            ncRNAs                            :: 12
            Pseudo Genes (total)              :: 188
            CDSs (without protein)            :: 188
            Pseudo Genes (ambiguous residues) :: 0 of 188
            Pseudo Genes (frameshifted)       :: 67 of 188
            Pseudo Genes (incomplete)         :: 128 of 188
            Pseudo Genes (internal stop)      :: 25 of 188
            Pseudo Genes (multiple problems)  :: 32 of 188
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP087628.1.
            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/
FEATURES             Location/Qualifiers
     source          1..1856
                     /organism="Klebsiella pneumoniae subsp. pneumoniae"
                     /mol_type="genomic DNA"
                     /strain="DD02280"
                     /host="Homo sapiens"
                     /sub_species="pneumoniae"
                     /db_xref="taxon:72407"
                     /plasmid="pDD02280-5"
                     /geo_loc_name="China:Shanghai"
                     /lat_lon="39.87 N 116.28 E"
                     /collection_date="2017-12-01"
                     /collected_by="Jiachun Su"
     gene            311..1798
                     /gene="ltrA"
                     /locus_tag="LMH50_RS29620"
                     /old_locus_tag="LMH50_29620"
     CDS             311..1798
                     /gene="ltrA"
                     /locus_tag="LMH50_RS29620"
                     /old_locus_tag="LMH50_29620"
                     /EC_number="2.7.7.49"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:YP_005226014.1"
                     /GO_function="GO:0003964 - RNA-directed DNA polymerase
                     activity [Evidence IEA]"
                     /GO_process="GO:0000373 - Group II intron splicing
                     [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="group II intron reverse transcriptase/maturase"
                     /protein_id="WP_004178082.1"
                     /translation="MMYGEEKSDSLIVAAKQANNPKGAESVERRSGAKGNAEQPHMRRT
                     QSRESMSQRLSRVREAAKQRKKERFTALFHLLTVEALEAAFLSLSRKAAAGVDGIRWMD
                     YAGNMKNNITDLHRRLHQGSYRAQPGRRHYIPKADGKQRPLGIASLEDKIVQYALVKIL
                     NAVYENDFMGFSYGFRPGRSQHDALDALATGLVRTNVNWVLDADISQFFDRVSHEWLIR
                     FTEHRIGDRRVIRLIRKWLTAGTSEEGQWRATEEGTPQGAVISPLLANIYLHYVFDLWA
                     HQWRRRYATGNVVMVRYADDIVIGFDKRYDARRFRIAMQRRLREFGLTVHPEKTRLMEF
                     GRFAAENRAIRGKGKPETFNFLGFTHISGKDRNGRFMLIRKTRRDRMTATLKAIKDGLR
                     RRWHYSIPEQGKWLRRVVQGYLNYHSVPGNFPTMQKFRTHVTNLWRRALRRRSQKDDTT
                     WTKANKLAAAWLPRVRVLHPWPVERFTARHPRQEPGA"
                     /name="ltrA"
ORIGIN
        1 gaccagcaat ccacaaggtc cccgagtcat gcgttgcata ccgcgaggta tggggcgaag
       61 cgttgacagg ggtgttgaca ggccagccat tgagccacga aatgtatatt aaattaccgg
      121 gtgccgacgt tgtactgtta acggaaggca acatcatagg gtgcgatact gcgagtgcca
      181 catggacccg gcggggtctg agaccctggc atgtcaatac gatctctacg cgggaaccgg
      241 gagatctccc ctctgaccat ctgccagtgt cggagatggc ccgcaccggg aagacgagga
      301 gtcatagccg gtgatgtacg gagaggagaa gtcggactcg ctcatagtag cggcgaagca
      361 ggcgaacaac ccgaaaggag cggagtcagt ggagcgaagg agcggggcca aggggaacgc
      421 ggaacagcca cacatgcgcc ggacacagag ccgggaaagc atgtcacaga ggctgtcacg
      481 cgtgcgggaa gctgcgaagc agcggaagaa agaacggttt acagcattgt tccacctgct
      541 gacagtcgaa gcactggaag ccgcattcct ctccctgagc aggaaagcgg ccgccggagt
      601 ggatggcatc aggtggatgg actacgccgg aaacatgaag aacaacataa cagatctgca
      661 ccggaggcta catcagggca gctacagggc gcagcccggc aggcgtcact acatcccaaa
      721 agcggatgga aaacaacgcc cgctcggcat cgcctcgctg gaggacaaga tcgtccagta
      781 tgcgctggtg aaaatcctga acgcagtcta tgaaaacgac tttatggggt tctcatacgg
      841 gttcagaccc gggcgaagcc agcacgatgc actggacgca ctggccacag ggctggtacg
      901 cactaacgta aactgggtac tggatgccga catcagtcag ttcttcgaca gggtgagcca
      961 cgaatggctg atcaggttca cagagcatcg gatcggcgac cggagggtaa tcaggctcat
     1021 acgtaagtgg ctcacagccg ggacgtcgga ggagggtcaa tggcgagcaa cggaggaagg
     1081 caccccacag ggtgcggtca tctcaccgct gctggcaaac atatacctcc actacgtctt
     1141 cgatctgtgg gcgcatcagt ggcgacgtcg ctatgccaca ggcaatgtgg taatggtcag
     1201 atacgccgat gacatcgtca tcgggttcga caaacgatac gatgcccggc gcttccgtat
     1261 agccatgcag cgcagactga gggagttcgg actcacggtt cacccggaga aaacccgtct
     1321 gatggagttc ggccgcttcg ctgccgaaaa ccgtgccatc aggggaaaag gcaaaccaga
     1381 aacgttcaac ttcctcgggt tcacgcacat cagcgggaaa gatcgcaacg gcaggttcat
     1441 gctgatacga aagacccgcc gggatcggat gacggcaact ctgaaagcca tcaaagacgg
     1501 tctgcgaagg cgctggcatt actcaatccc cgaacaggga aaatggctca ggagagtggt
     1561 tcagggatac ctgaactatc actcggtacc gggcaacttc cccaccatgc agaagttcag
     1621 gacacacgta acaaacctct ggcgccgggc gctcaggcgc aggagccaga aggatgatac
     1681 gacctggacg aaagcaaaca aactggcagc cgcatggcta ccaagggttc gggttcttca
     1741 tccatggcct gtggagcggt tcaccgccag acacccgagg caggagcccg gtgcgtaaat
     1801 cgcgcacgcc gggatctgtg cggggggtat ccggtaacgg gtatccctac cgcgac
//
