LOCUS       CP128695                5521 bp    DNA     circular BCT 03-JUL-2023
DEFINITION  Klebsiella pneumoniae strain KPN482 plasmid pKPN482_5, complete
            sequence.
ACCESSION   CP128695
VERSION     CP128695.1
DBLINK      BioProject: PRJNA788509
            BioSample: SAMN35878166
KEYWORDS    .
SOURCE      Klebsiella pneumoniae
  ORGANISM  Klebsiella pneumoniae
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Klebsiella/Raoultella group; Klebsiella.
REFERENCE   1  (bases 1 to 5521)
  AUTHORS   Kochan,T.
  TITLE     Klebsiella pneumoniae Clinical Isolates with Features of Both
            Multidrug-Resistance and Hypervirulence Have Unexpectedly Low
            Virulence
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 5521)
  AUTHORS   Kochan,T.
  TITLE     Direct Submission
  JOURNAL   Submitted (23-JUN-2023) Microbiology & Immunology, Northwestern
            University, 303 E Chicago Ave, Ward 6-035, Chicago, IL 60611, USA
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: trycycler v. v0.4.1
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 45.4541809495107x
            Sequencing Technology :: Oxford Nanopore MinION/GridION, Illumina
            NovaSeq/MiSeq
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI
            Annotation Date                   :: 06/26/2023 13:42:59
            Annotation Pipeline :: NCBI Prokaryotic Genome Annotation Pipeline
            (PGAP)
            Annotation Method :: Best-placed reference protein set; GeneMarkS-2+
            Annotation Software revision      :: 6.5
            Features Annotated                :: Gene; CDS; rRNA; tRNA; ncRNA
            Genes (total)                     :: 5,620
            CDSs (total)                      :: 5,500
            Genes (coding)                    :: 5,321
            CDSs (with protein)               :: 5,321
            Genes (RNA)                       :: 120
            rRNAs                             :: 9, 8, 8 (5S, 16S, 23S)
            complete rRNAs                    :: 9, 8, 8 (5S, 16S, 23S)
            tRNAs                             :: 84
            ncRNAs                            :: 11
            Pseudo Genes (total)              :: 179
            CDSs (without protein)            :: 179
            Pseudo Genes (ambiguous residues) :: 0 of 179
            Pseudo Genes (frameshifted)       :: 77 of 179
            Pseudo Genes (incomplete)         :: 116 of 179
            Pseudo Genes (internal stop)      :: 29 of 179
            Pseudo Genes (multiple problems)  :: 35 of 179
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            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..5521
                     /organism="Klebsiella pneumoniae"
                     /mol_type="genomic DNA"
                     /strain="KPN482"
                     /isolation_source="respiratory"
                     /host="Homo sapiens"
                     /db_xref="taxon:573"
                     /plasmid="pKPN482_5"
                     /geo_loc_name="USA:Houston"
                     /lat_lon="29.710689 N 95.400586 W"
                     /collection_date="2012-10"
                     /collected_by="Houston Methodist Hospital"
     gene            1..114
                     /locus_tag="QU720_28070"
     CDS             1..114
                     /locus_tag="QU720_28070"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001422066.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="replication initiation protein"
                     /protein_id="WJU05040.1"
                     /translation="MHEPPVQSDRCALSGNYHLESNPERYEKTPLAAAIGN"
                     /name="replication initiation protein"
     gene            415..974
                     /locus_tag="QU720_28075"
                     /pseudo=""
     CDS             415..974
                     /locus_tag="QU720_28075"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_086558267.1"
                     /note="frameshifted; incomplete; partial on complete
                     genome; missing C-terminus; Derived by automated
                     computational analysis using gene prediction method:
                     Protein Homology. GO_function: GO:0004803 - transposase
                     activity [Evidence IEA]"
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="IS1 family transposase"
                     /name="IS1 family transposase"
     gene            1210..1374
                     /locus_tag="QU720_28080"
                     /pseudo=""
     CDS             1210..1374
                     /locus_tag="QU720_28080"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_076612230.1"
                     /note="incomplete; partial on complete genome; missing
                     N-terminus; Derived by automated computational analysis
                     using gene prediction method: Protein Homology.
                     GO_function: GO:0003677 - DNA binding [Evidence IEA];
                     GO_function: GO:0004803 - transposase activity [Evidence
                     IEA]; GO_process: GO:0006313 - DNA transposition [Evidence
                     IEA]"
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="IS1 family transposase"
                     /name="IS1 family transposase"
     gene            complement(1515..1688)
                     /locus_tag="QU720_28085"
     CDS             complement(1515..1688)
                     /locus_tag="QU720_28085"
                     /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="WJU05041.1"
                     /translation="MSEDIGKVVDIFNEFTKVELPGGGGLETDSPVVEAAVAVGVLGAA
                     AYGLYKLFSSDD"
                     /name="hypothetical protein"
     gene            2298..3233
                     /locus_tag="QU720_28090"
     CDS             2298..3233
                     /locus_tag="QU720_28090"
                     /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="WJU05042.1"
                     /translation="MTAQDLINVLTILKANDSTSFSKIQRALKMSISQLEGIIDGLTAM
                     GIVYKSSFTSYSLTELTSKPVVSDGVRKAFEDIITNRGTYLSEELLQKVSTPFIPLMTH
                     EYKNAPVKVMIVGQETLGMEDAFSTIVSVDDYINESIESFNKFNFGEDLRNSHFWYAFD
                     EVVKYFNLPSRRHAYWTNLHKFQLIENDGDSVSISKLPSKDIMTMIHMQRELFLAEIKD
                     TKPDIIIYFTGGQTWVLDHYLNNGKKLAVKAIDERSHLGIIQTEFLHCPIAICTDHPSR
                     RGYTQAIVDHRANLLKYAADKFHASESAWF"
                     /name="hypothetical protein"
     gene            complement(4038..4448)
                     /locus_tag="QU720_28095"
     CDS             complement(4038..4448)
                     /locus_tag="QU720_28095"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:YP_005229777.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="helix-turn-helix domain-containing protein"
                     /protein_id="WJU05038.1"
                     /translation="MARVSISEAARLVKVSRPTIYKMINSGKLSYTSVVKHGKGIKVID
                     TSELIRVFGSLDGVIDDVKSDAESTGINSVGFHDLQHRIALLEAENDGLKGAVKARDEH
                     IDSLRQAMQLLEHKHEPSSPPHSPWWKFWKKS"
                     /name="helix-turn-helix domain-containing protein"
     gene            complement(4448..4639)
                     /locus_tag="QU720_28100"
     CDS             complement(4448..4639)
                     /locus_tag="QU720_28100"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000166328.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="Rop family plasmid primer RNA-binding protein"
                     /protein_id="WJU05039.1"
                     /translation="MTKQQKTALNMAKFIQNQSLLLLEKLNELDLDAEADLCEKLHDDA
                     EHLFRTLSSRLDELQDGN"
                     /name="Rop family plasmid primer RNA-binding protein"
     Typing          complement(4987..5160)
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="2.5600000000000002e-86"
     Typing          2..132
                     /name="rep_cluster_2335"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="91.729"
                     /coverage="98.0"
                     /evalue="7.36e-44"
     Typing          5261..5521
                     /name="rep_cluster_2373"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="95.057"
                     /coverage="87.0"
                     /evalue="1.46e-112"
ORIGIN
        1 atgcacgaac cccccgttca gtccgaccgc tgcgccttat ccggtaacta tcatcttgag
       61 tccaacccgg aaaggtacga aaaaacgcca ctggcagcag ccattggtaa ctgagatgtg
      121 cgagagattt atctggagtt cttgaagtgg gagcctgaga acggctacac tggaaggaca
      181 gttttggtga ctcgtctcgc acaagacagt tacctggtta agcagttccc caactgacct
      241 aaccttcgat caaaccacct ccccaggtgg ttttttcgtt tcttggagaa gagactacga
      301 cgacaaatga cggatctcaa gaagatcctt ttaacgtaca aaaatttccg ttctccaaag
      361 gtgatgctgc caacttactg atttagtgta tgatggtgtt ttttaggtgc tccagtggct
      421 tctgtttcta tcagctgtcc ctcctgttca gctactgacg gggtggtgcg taacggcaaa
      481 agcactgccg gacatcagcg ctatctctgc tctcactgcc gtaaaacatg gcagctacag
      541 ttcacttaca ccgcctctca gcccggtacg caccagaaaa tcattgatat ggccatgaat
      601 ggcgttggat gccgggcaac cgcccgcatt atgggcgttg gcctcaacac gattttacgt
      661 cacttaaaaa actcagaccg cagtcggtaa cctcgcgcat acaaccgggc agtgatgtga
      721 ttgtctgcgc tgaaatggac gaacagtggg gctacgtcgg tgctaaatca cgtcagcgct
      781 ggctgtttta cgcgtatgac aggatacgga ggacggttgt ggcgcacgtc ttcggtgaac
      841 gcactctggc cacactggag cgtcttctga gcctgctgtc ggcctttgag gtcgtggtat
      901 ggatgacgga tggctggccg ctgtatgaat cacgcctgaa gggaaagctg cacgttaaca
      961 gcaagcgtta cactggggtc agtttggaga tcggaaattt ttgtacgtta agcgcattat
     1021 ttaaccaatc ttggttcgta aggggttgat tttgcgtcag tggctatcgc ttttaagttg
     1081 tcgctcttgc agtatcgcat ttaggttatc cgattaaggt caaacctctg aaaatgccgt
     1141 atagcgcggg agtacaccct attgctatag gtaagtctgt tcaaaaaaca ggcttgccgt
     1201 acaataattc tctatatcca aactgacccc tacactcaac gcattgagcg gcataacctg
     1261 aatctgaggc agcacctggc acggcatgga cggaagtcgc tgtcgttctc aaaatcggtg
     1321 gagctgtatg acaaagtcat cgggcattat ctgaacataa aacactatca ataagttgga
     1381 gtcattacct gaaatggcaa cagatagctg attctttggg ttgttcgtat catgcagccg
     1441 ttgcactata taagcgttat gagagattag atctaaatga aaaggcgggg aaataaatcc
     1501 ccaccgttaa ataattaatc atcactacta aatagcttat aaagcccata tgctgcggca
     1561 cctaaaacac caacagcaac agcagcctct acaacagggc tatcggtctc taaacctcct
     1621 ccaccaggaa gttcaacctt cgtaaattca ttaaaaatat caacaacttt accaatatct
     1681 tcactcataa caccctcctt tttgaagaag tattttactt ctaatcaaaa aggtaaacca
     1741 tatcaaccct tcaaactacc aaaataaatt ttgttagttt tcagcgtttt tatttaaata
     1801 atgttcaccc ttgattttta acatgttttt ttgtgattct gtcatgttat caacatacaa
     1861 caatgcacct attacaagat ttctatttcc atcttataat ttaagacact ctgccccaag
     1921 aacgattaaa tcatgtgttc tttttcttct atcttcgttt attttcttct ttcttagcat
     1981 gttcaaccta ttttgggctg atgctatttg ctgatctaaa tttttactca taatcagaaa
     2041 caccaagata attaccaaca ttcataagaa caaaaacata cgctaaattt tctaacacac
     2101 taatctctat aagattataa tcaacagaag cattagcttt aaaatattca attcccaaaa
     2161 agacaacatc cctaactatt ttaataatat aagaatccct ggtgatgctg ccaacttact
     2221 gatttagtgt actgcgaccg tcagaatgag ttaaacgcgt atctacattg aagcagttca
     2281 atatgaggaa aacaggaatg acagcacaag atttaatcaa cgttctcact attcttaagg
     2341 ccaacgactc aaccagtttt agcaagattc aacgcgcgtt aaagatgagt atttcgcagt
     2401 tggagggcat cattgatggg ttaactgcaa tgggaatagt gtataaatca tcattcactt
     2461 catacagcct tactgagtta acctctaaac ctgttgttag tgacggtgta agaaaggcat
     2521 tcgaagatat cattaccaat cgcggtactt acctgtcaga agaactacta caaaaggtaa
     2581 gtacaccatt catcccactg atgacgcacg aatacaaaaa tgccccagtt aaagtgatga
     2641 tcgtggggca agaaactctg ggaatggaag atgctttcag taccatcgtt tcggtcgatg
     2701 actacattaa tgagagcatt gaatccttca ataaattcaa ttttggtgaa gatttaagga
     2761 atagccactt ttggtatgca tttgatgaag tagtaaagta ttttaaccta ccatccagaa
     2821 ggcatgctta ttggactaat cttcataagt ttcaattaat tgaaaatgat ggagatagtg
     2881 tcagcatttc caaactacct tcaaaagata tcatgacaat gattcatatg cagcgtgaat
     2941 tattcttggc tgaaattaaa gataccaagc cagatatcat catctacttc acgggtgggc
     3001 aaacctgggt gttagatcat tatctaaaca atggtaaaaa attagcagtt aaggcaatag
     3061 atgaacgctc gcatctgggg attatccaga cagaattttt gcattgccca atcgctatat
     3121 gtaccgacca tcctagtaga aggggatata ctcaagccat cgtagatcat agagctaatc
     3181 tgcttaaata tgctgctgac aaatttcatg caagtgaatc ggcatggttc tagcgaacac
     3241 atgtcaccga cagaatatga aaaccagtat tatcaacggc tcggaagtgt ctaaattatc
     3301 cgtggcgatt caatttacca taacatccgt tgcgtgcacc gcctcagagc ctctgaggac
     3361 gtttctgacg ggaaaccggt aaaacaggca acaaaccacc cgaaaacccg ccagaaacgc
     3421 gcaggctctg tttttacggc atgcatgagt atgcgcacaa gtgcatagcg cggaaattca
     3481 cgccattcag ccggggtaag tcctgtttcc ggcgttcttc ccatccgaaa acggtgaacg
     3541 gggacgcaat ttattgcgtg gccgtgaagc gttgccggcg cagccggaaa accggttttc
     3601 agcacgttca ggaatcgggt tcgtcgacgg ccggcaatca cgttatggca agtcgccgga
     3661 cgactcaccg gcgattcgac tcgtgacttg actctagagt caccgcggtc aaaaaaacgc
     3721 caaagcgacg attcgactct agagtcaagt cgtcataagt tactgatagt gtggagtgag
     3781 tcgtcgatga ctctatgacg agtcgtcggc aagtcgtaca cgaatcaccg acgacttgga
     3841 ttgaccttac agaaggtaat actgcgtaat ttaataaaac ctaaccaact gataataagg
     3901 agttatctgc aaaattttaa ttttgcgtgg tgtgtgggta tttttcgtgg tgaggagtgt
     3961 tcccggatct ggcgattttt gggaaggttc aggaacgccc cgggatggcc ggagaggaaa
     4021 actcaagcat ggcgggatca ggattttttc cagaatttcc accacgggga atggggtggt
     4081 gaagaaggtt cgtgcttgtg ctccagaagc tgcatagcct gacgaaggga atcaatatgc
     4141 tcatctcgag ccttaacagc ccctttaaga ccatcgtttt cagcttcaag taaagcgatt
     4201 ctatgttgta aatcatgaaa accaacgctg ttaatacctg tagattctgc gtcacttttt
     4261 acatcatcga tgacaccatc aagagaacca aacactctaa taagctctga tgtatcaata
     4321 actttaatac ccttcccgtg ctttacaaca gaggtgtaac ttaacttacc actgttaatc
     4381 atcttgtaaa tagtagggcg actaacctta acaagccgtg ctgcttcact aatagacact
     4441 ctggccatca gttaccatcc tgtaattcat ccagtctcga ggacagtgta cggaaaagat
     4501 gctccgcatc atcgtggagt ttctcacaaa ggtcggcctc agcatcgaga tcaagctcgt
     4561 taagcttctc cagcaggagc agagactgat tctggatgaa tttagccatg ttcagcgctg
     4621 ttttctgttg tttcgtcata agggacctca gagcatcaat gctcagtgta aaaccggtaa
     4681 gggggtcgga tgtacgaatg gttcagagaa cggatctgag gtaatcctgt agttattttg
     4741 tagtttatct gtagtcatcg cactaaaaat caggattaag tcatcagctt ttgtagtctt
     4801 tctgtagttt acctgtagtc cggaaaaaca atccgttcat gcgagcatga acgaggtcgt
     4861 tagtaacctg cgccattaaa tcaaaaaggt catattcgcc gggaagctgc gtatcagtcg
     4921 aatcccgttg ttcatcatat tcagatggca tggggtgata tccagtagct gagaggttgt
     4981 tagagggttt cggggcgcag ccctgaacca gtcacgtagc gctagcggag tgtaaactgg
     5041 cttattatgt tggcacgggc acggaaatca gtgaagtgct tcatgtggca gaagaaaaaa
     5101 ggcggcaccg gcgcgtaagc agaatatgcg atacaggaga tattccgctt cctcgctcac
     5161 tgactcgctc cgctcggtcg ttcggctgcg gcgagcagta ccagcttact ggcgggacgg
     5221 aaatttcctg gtagatgcca ggaaggaacg taacagggaa acaataacgc cgcggcaaag
     5281 ccgtttttcc ataggctccg cccccctgac gagcatcaca gaatctgaca ctcaaatcag
     5341 tggtggcgaa acccgacagg actataaaga tcccaggcgt ttccccctgg tagctccctc
     5401 gtgcgctctc ctgttcctgc ctttcggtgt accggtgtca ttccgctgtt atggccgcgt
     5461 ttatctcatt ccacgcctga cactcagttc cgggtaggca gttcgctcca agctggactg
     5521 t
//
