LOCUS       NZ_CP090132             5651 bp    DNA     circular CON 03-DEC-2023
DEFINITION  Klebsiella pneumoniae strain KP46 plasmid pKP46_6, complete
            sequence.
ACCESSION   NZ_CP090132
VERSION     NZ_CP090132.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN24255899
            Assembly: GCF_021397585.1
KEYWORDS    RefSeq.
SOURCE      Klebsiella pneumoniae
  ORGANISM  Klebsiella pneumoniae
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Klebsiella/Raoultella group; Klebsiella.
REFERENCE   1  (bases 1 to 5651)
  AUTHORS   Sun,Q.
  TITLE     Complete genome sequence of a Klebsiella pneumoniae isolate KP46
            carrying blaKPC-2 and blaNDM-1 genes
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 5651)
  AUTHORS   Sun,Q.
  TITLE     Direct Submission
  JOURNAL   Submitted (21-DEC-2021) Department of Clinical laboratory, Sir Run
            Run Shaw Hospital, School of Medicine, Zhejiang University, 3
            Qingchun East Road, Hangzhou, Zhejiang 310016, China
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: Unicycler v. 0.4.8
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 100.0x
            Sequencing Technology :: Illumina NovaSeq; Oxford Nanopore GridION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 12/03/2023 03:56:12
            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)                     :: 5,581
            CDSs (total)                      :: 5,457
            Genes (coding)                    :: 5,305
            CDSs (with protein)               :: 5,305
            Genes (RNA)                       :: 124
            rRNAs                             :: 9, 8, 8 (5S, 16S, 23S)
            complete rRNAs                    :: 9, 8, 8 (5S, 16S, 23S)
            tRNAs                             :: 87
            ncRNAs                            :: 12
            Pseudo Genes (total)              :: 152
            CDSs (without protein)            :: 152
            Pseudo Genes (ambiguous residues) :: 0 of 152
            Pseudo Genes (frameshifted)       :: 54 of 152
            Pseudo Genes (incomplete)         :: 102 of 152
            Pseudo Genes (internal stop)      :: 20 of 152
            Pseudo Genes (multiple problems)  :: 20 of 152
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP090132.1.
            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..5651
                     /organism="Klebsiella pneumoniae"
                     /mol_type="genomic DNA"
                     /strain="KP46"
                     /isolation_source="Cerebral spinal fluid"
                     /host="Homo sapiens"
                     /db_xref="taxon:573"
                     /plasmid="pKP46_6"
                     /geo_loc_name="China: Hangzhou"
                     /collection_date="2017-12-14"
                     /collected_by="Qingyang Sun"
     gene            join(5321..5651,1..605)
                     /locus_tag="LWR79_RS27840"
                     /old_locus_tag="LWR79_27840"
     CDS             join(5321..5651,1..605)
                     /locus_tag="LWR79_RS27840"
                     /old_locus_tag="LWR79_27840"
                     /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="MobA/MobL family protein"
                     /protein_id="WP_045626452.1"
                     /translation="MATYHLSVKFGGKGKALAHASYITREDKFSQRQDLEHTEHGNMPE
                     WARDEPAHFWQAADAFERANGSTYREIEIALPRELNEAQRLALVRDFVKQETGDKHAWT
                     FAIHNPKASIDGGEQPHAHIMMSQRVNDGIERSPEQYFRRYNAKFPARGGARKDSGHNL
                     TPTEQKQALKALRERWERTHNAHMKRYGFEQGFIDSRSLKTQGIDRKPEQHLGFEAAGR
                     LDDSQRQDIKDSRTFSVVDVPEQAKHIDHSDRSWMNASGIEVNRKELVRSLTHDISQQY
                     GREMAARVTKQGNVEIERVKSLSRGFSISR"
                     /name="MobA/MobL family protein"
     gene            608..1138
                     /locus_tag="LWR79_RS27845"
                     /old_locus_tag="LWR79_27845"
     CDS             608..1138
                     /locus_tag="LWR79_RS27845"
                     /old_locus_tag="LWR79_27845"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000168766.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_012634455.1"
                     /translation="MASTEEKLLTLLLSAEHLKEAAKEQQKAVADSLAVARETLKGYRE
                     ISDSVAQQVRDEVRQEVQKMDVAGLIGERISADFQRLEKSVGNMKINADALDKEISIIR
                     SNIIAEYNTLRGYSWKWFAGVAVAFVVLIFATSWFVKTELQDNYNASAAVYQKVADLEK
                     LLTTEQKPEKKKN"
                     /name="hypothetical protein"
     gene            complement(1877..2574)
                     /locus_tag="LWR79_RS27850"
                     /old_locus_tag="LWR79_27850"
     CDS             complement(join(1877..2325,2325..2574))
                     /locus_tag="LWR79_RS27850"
                     /old_locus_tag="LWR79_27850"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_086558260.1"
                     /ribosomal_slippage=""
                     /GO_function="GO:0004803 - transposase activity [Evidence
                     IEA]"
                     /GO_process="GO:0006313 - DNA transposition [Evidence IEA]"
                     /note="programmed frameshift; Derived by automated
                     computational analysis using gene prediction method:
                     Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="IS1-like element IS1B family transposase"
                     /protein_id="WP_095033700.1"
                     /translation="MASVSISCPSCSATDGVVRNGKSTAGHQRYLCSHCRKTWQLQFTY
                     TASQPGTHQKIIDMAMNGVGCRATARIMGVGLNTIFRHFKKLRPQSVTSRIQPGSDVIV
                     CAEMDEQWGYVGAKSRQRWLFYAYDRLRKTVVAHVFGERTMATLGRLMSLLSPFDVVIW
                     MTDGWPLYESRLKGKLHVISKRYTQRIERHNLNLRQHLARLGRKSLSFSKSVELHDKVI
                     GHYLNIKHYQ"
                     /name="IS1-like element IS1B family transposase"
     gene            <2632..2931
                     /locus_tag="LWR79_RS27855"
                     /old_locus_tag="LWR79_27855"
                     /pseudo=""
     CDS             <2632..2931
                     /locus_tag="LWR79_RS27855"
                     /old_locus_tag="LWR79_27855"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_004821790.1"
                     /note="incomplete; partial in the middle of a contig;
                     missing N-terminus; Derived by automated computational
                     analysis using gene prediction method: Protein Homology."
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="enoyl-CoA hydratase/isomerase family protein"
                     /name="enoyl-CoA hydratase/isomerase family protein"
     gene            3177..3956
                     /locus_tag="LWR79_RS27860"
                     /old_locus_tag="LWR79_27860"
     CDS             3177..3956
                     /locus_tag="LWR79_RS27860"
                     /old_locus_tag="LWR79_27860"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000422636.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="APH(3')-VI family aminoglycoside
                     O-phosphotransferase"
                     /protein_id="WP_109018074.1"
                     /translation="MELPNIIQQFIGNSVLEPNKIGQSPSDVYSFNRNNETFFLKRSST
                     LYTETTYSVSREAKMMSWLSDKLKVPELIMTFQDEQFEFMITKAINAKPISALFLTEQE
                     LLSIYKETLNQLNAVAIFDCPFISSIDHRLKESKFFIDNQLLDEIDQDDFEAELWGDHK
                     TYLSLWNELNETRVEERLVFSHGDITDSNIFIDKSGEIYFLDLGRAGLADEFVDISFVE
                     RCLREDVSEETAKIFLKHLKNDMPDKRNYFLKLDELN"
                     /name="APH(3')-VI family aminoglycoside
                     O-phosphotransferase"
     gene            complement(4768..5154)
                     /locus_tag="LWR79_RS27865"
                     /old_locus_tag="LWR79_27865"
     CDS             complement(4768..5154)
                     /locus_tag="LWR79_RS27865"
                     /old_locus_tag="LWR79_27865"
                     /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_045282373.1"
                     /translation="MRISNVEWLKKRIAFIRKLGEKTARQRQIIDLLDDEASLSETERR
                     LLHVLATAEKNALQERDAAQKKAVQARISGQKNRRERNHRLFLAAGLMIDAGLVDTKTG
                     ELNFDHEKLLTALKRVRYDLETSA"
                     /name="hypothetical protein"
     ARG             3178..3953
                     /name="aph(3')-VIb"
                     /gene="aph(3')-VIb"
                     /gene_name="aminoglycoside O-phosphotransferase
                     APH(3')-VIb"
                     /tool="amrfinderplus"
                     /drug_class="AMINOGLYCOSIDE"
                     /identity="98.07"
                     /coverage="100.0"
     Typing          4..602
                     /name="MOBQ"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="98.5"
                     /coverage="99.0"
                     /evalue="3.08e-128"
     Typing          5322..5650
                     /name="MOBQ"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="90.0"
                     /coverage="99.0"
                     /evalue="4.29e-61"
ORIGIN
        1 aagccagcat tgacggcggc gaacagccgc acgcccatat catgatgagc cagcgcgtca
       61 atgacggtat tgagcgcagt cccgaacagt atttcaggcg ctataacgcc aaatttccgg
      121 cgcgtggcgg cgcgcgcaag gactcagggc ataatttaac ccctacagaa caaaaacagg
      181 cactgaaagc cctgcgggag cgctgggagc gtacgcacaa cgcgcatatg aaacgatatg
      241 gctttgagca gggttttatt gatagccggt cactgaaaac acagggtatc gaccggaaac
      301 cggaacagca tctcggtttt gaagcagccg gacgactgga cgacagccag aggcaggata
      361 ttaaagacag ccggacgttt tcagtcgtgg atgtgcctga acaggcgaaa catatcgacc
      421 acagcgaccg tagctggatg aatgccagcg gtatcgaggt aaaccggaag gaactggtca
      481 gatctctgac gcatgatatc tcgcagcagt acgggcggga gatggctgca cgggtcacaa
      541 aacagggaaa tgttgaaata gagcgcgtga aatccctgtc acgcggattt tccataagca
      601 ggtaactatg gcgagcaccg aagaaaaact tctcacactc ctgctgtcgg cggagcatct
      661 gaaagaggcc gcaaaagagc agcagaaagc cgtggcggat tcgctggcgg tggcaaggga
      721 aaccctgaaa ggctaccggg aaatatcgga cagtgtggca cagcaggtaa gggatgaagt
      781 ccggcaggaa gtgcagaaaa tggatgttgc ggggctgatt ggcgagcgta tcagcgctga
      841 ttttcagcgt ctggaaaaat ccgtcgggaa catgaaaatc aatgcggacg cgctggacaa
      901 ggaaatttcc attatccgca gtaacatcat cgcggagtac aacacgctgc ggggttacag
      961 ctggaagtgg tttgctgggg ttgcggttgc ctttgtcgta ctgatatttg ccacaagctg
     1021 gtttgtgaaa acggaactac aggacaatta caacgcgtct gctgccgtct atcagaaagt
     1081 ggcagacctt gaaaagctgc tgacaacgga acagaaaccg gaaaagaaaa agaactgacg
     1141 cgctgcgctt gtccaacgcc tcacgttcgc acaataaatt gcgcacccgt tcaccgtttt
     1201 cagccgagtt tggggcgtct tttgagactt ccggcctgaa ttcaggccgg aagttctcgc
     1261 cagtcagtca ggtgcatggt tatgcatggg gctgaaaatc acggtatgcg attctgagcg
     1321 gttttcggtg agaagccggg ggtttttatg gctcaggact taaaaccgcc ctgagagcct
     1381 ctgaggcggt gcgggcaacg gatgttatgg taaatccggt ggctttgacg tgcctgccgt
     1441 tgtgtaccgt cgtgagtgaa aataattata ttgttcgaag aacagcgctt tttggccgga
     1501 gaaaagcagt tctgcaaacg atggtatatc gatatgagtt cttttggcat taatccaggc
     1561 aagacgccgg gcaataagcg taatattccg gatgttactt atttccattt ctgtcaacag
     1621 catccccccc cacgccggag aataaaaaag ccgcctgttc catcggcaag ccctacatca
     1681 agggaaacta cgtcttacga ttcgttttga accgggacgc tttgttgctg cgaatcacta
     1741 accagataat ccacgttttg tgagtgggtt taggttaagg cttcaataga acaataatag
     1801 cgttaagtga ttagggcaac ctgtgattgc taaaatgatg aagtcttcac atcatttcgg
     1861 tggtaatgac tccaacttac tgatagtgtt ttatgttcag ataatgcccg atgactttgt
     1921 catgcagctc caccgatttt gagaacgaca gcgacttccg tcccagccgt gccaggtgct
     1981 gcctcagatt caggttatgc cgctcaattc gctgcgtata tcgcttgctg attacgtgca
     2041 gctttccctt caggcgggat tcatacagcg gccagccatc cgtcatccat atcaccacgt
     2101 caaagggtga cagcaggctc ataagacgcc ccagcgtcgc catcgtgcgt tcaccgaata
     2161 cgtgcgcaac aaccgtcttc cggagcctgt catacgcgta aaacagccag cgctggcgcg
     2221 atttagcccc gacgtatccc cactgttcgt ccatttccgc gcagacgatg acgtcactgc
     2281 ccggctgtat gcgcgaggtt accgactgcg gcctgagttt tttaaatggc ggaaaatcgt
     2341 gttgaggcca acgcccataa tgcgggcggt tgcccggcat ccaacgccat tcatggccat
     2401 atcaatgatt ttctggtgcg taccgggttg agaagcggtg taagtgaact gcagttgcca
     2461 tgttttacgg cagtgagagc agagatagcg ctgatgtccg gcggtgcttt tgccgttacg
     2521 caccaccccg tcagtagctg aacaggaggg acagctgata gaaacagaag ccactggagc
     2581 acctcaaaaa caccatcata cactaaatca gtaagttggc agcatcacct gctagccgaa
     2641 cgatatggtt gggtaaatcg tgcgcttccg gcaaatgagt tagacgcttt tgttcatcgc
     2701 atcgccacaa atattgcagc tttacctgaa ggggtcatcg ccgctgcaaa gaaagcaatc
     2761 ccaccaacgg atttaagtga agacttcctt cgagagcaca aggcatgggc tggtctgttt
     2821 gcgcgtccgg ctgctgaaaa actcattcgt ggcggcttgc aggcaggtgc tcaaacaaaa
     2881 gtgggcgaac aggatttgga gcaactactc cgcgatttgt ctgcatcctg aggtcttgct
     2941 gctgtctaat attctgctct agcttattct tgagatttga gacagagaaa tacagcaacc
     3001 cattttcctt aagcctagcg ctatttatgc aattgagagg taatgacaaa agtttgatgc
     3061 attgaccctc tatagacaat aagccatatt tttgctacag tgaacctaat taagatcatc
     3121 tatttactag gcctcgcatt tgcgaggttt ttaatgctga ataaaaggaa aacttgatgg
     3181 aattgcctaa tattattcaa caatttattg gaaacagcgt tttagagcca aataaaattg
     3241 gtcagtcgcc atcggatgtt tattctttta atcgaaataa tgaaactttt tttcttaagc
     3301 gatctagcac tttatataca gagaccacat acagtgtctc tcgtgaagcg aaaatgatga
     3361 gttggctctc tgataaatta aaggtgcctg aactcatcat gacttttcag gatgagcagt
     3421 ttgaattcat gatcactaaa gcgatcaatg caaaaccaat ttcagcgctt tttttaacag
     3481 agcaagaatt gctttctatc tataaggaaa cactcaatca gttaaatgca gttgctattt
     3541 ttgattgccc atttatttca agcattgatc atcggttaaa agagtcaaaa ttttttattg
     3601 ataaccaact ccttgacgag atagatcaag atgattttga ggctgaatta tggggagacc
     3661 ataaaactta cctaagtctt tggaatgagt taaatgagac tcgtgttgaa gaaagattgg
     3721 ttttttctca tggcgatatc acggatagta atatttttat agataaatct ggtgaaattt
     3781 actttttaga tcttggtcgt gctggattag cagatgaatt tgtagatata tcttttgttg
     3841 aacgttgcct aagagaggat gtatctgagg aaactgctaa aatattttta aagcatttaa
     3901 aaaacgatat gcctgacaaa aggaattatt ttttaaaact tgatgaattg aattaactcc
     3961 aagcaatatc taaaaatact tagctgtatt tttaagttgc taatttttaa ataaataagt
     4021 gaaaaaaggt aatgctgtca acctgttgat gactatttta atctgttgtc attcaatcct
     4081 tgtaacatca ggatgatcct ggtgtcagtg aaaatacgaa atcaacacgt tggtatcatt
     4141 acccatttcg gtgaaggcga tatgtgttac accacaaccc ggatttgaga gtcgcaaacc
     4201 catattaggg caaagaaagc ctaatgcccc cgtggtgggt acaccagaaa acggggagcg
     4261 aagcgaccag catcaggccg ttcgtatgct gcttcgattt tgtgggtgtt gcgccagacc
     4321 ttggcaatca cgcttcaccg caaccgctgc cttcactctc actttatcag gtacgttatt
     4381 ggttaacgtg agaccgggta gagccagctt ctttcccgag ctggtcaggt tcccaccgct
     4441 tgcctgttta tcctgccgga gtccggggcg tagacctgag agtcaaggtg cagatatggg
     4501 tttaatgtcg ttgaatggta ttaagctggt agtgacattc ctagccagcc ctgctaggat
     4561 ttgattgtga cgtctgatcc tggcaggtat ctgcaagaat tagagtactc aagccccgtg
     4621 attctgtcac ggggcttttg tacatctgga gcaagaaaat tcatgctcct atccgaaaat
     4681 ccctaccgct cgccgcagcc gaacgaccga gcgacgcgag tcagtgagcg aggaagcggc
     4741 atttctccgg ccttgcagaa tgcacgttca cgccgatgtt tccagatcgt agcgtacccg
     4801 tttcagcgca gtcagtaatt tttcgtggtc aaaattcaac tcacccgttt ttgtatcaac
     4861 cagtcccgcg tcaatcatca gaccagccgc cagaaacagt ctgtgattgc gttccctgcg
     4921 gtttttctgc cctgaaatcc gcgcctgaac cgcctttttc tgtgcggcat cccgttcctg
     4981 caacgcgttt ttttcagcgg ttgccagaac gtggagcagt cgtctttcag tctcactgag
     5041 cgaagcttca tcatccagca gatcgataat ctgccgttgc cgtgccgttt tttctcccag
     5101 ctttctgatg aaggctatgc gctttttaag ccattcgacg ttactgatcc gcatcgttta
     5161 acttccccat cccgatattt ccgacgggga aagtatataa cttgcggtca gaagtcgcat
     5221 gacttatctt tactcataat tctttaaatt agagtaaagc gcacttatat gtttctccct
     5281 gcgggcagaa acagtgcgcc ctgccggggg ctgacacaac atggcaacgt atcatctcag
     5341 cgtgaaattt ggcggcaagg gtaaagccct tgctcatgcc agttacatta cgcgggaaga
     5401 taagttcagc cagcgccagg atctcgagca caccgaacac ggcaatatgc cggaatgggc
     5461 gagagatgaa cccgctcatt tctggcaggc tgcggatgcg ttcgaacgtg ccaacggttc
     5521 aacgtacagg gaaattgaga tcgctctacc ccgcgagctg aatgaagcgc agcggctggc
     5581 gcttgtccgg gattttgtga agcaggaaac gggcgacaaa catgcatgga cgtttgcgat
     5641 ccacaatccg a
//
