LOCUS       NZ_CP132644             6141 bp    DNA     circular CON 24-AUG-2023
DEFINITION  Klebsiella pneumoniae strain 589376 plasmid p6, complete sequence.
ACCESSION   NZ_CP132644
VERSION     NZ_CP132644.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN36071305
            Assembly: GCF_030845595.1
KEYWORDS    RefSeq.
SOURCE      Klebsiella pneumoniae
  ORGANISM  Klebsiella pneumoniae
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Klebsiella/Raoultella group; Klebsiella.
REFERENCE   1  (bases 1 to 6141)
  AUTHORS   Luo,T.
  TITLE     Differentiation of hypervirulent and classical Klebsiella pneumoniae
            with acquired drug resistance
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 6141)
  AUTHORS   Luo,T.
  TITLE     Direct Submission
  JOURNAL   Submitted (03-JUL-2023) Walter Reed Army Institute of Research, MRSN
            BI Team, 503 Robert Grant Ave, Silver Spring, MD 20910, USA
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: Trycycler v. 0.5.3
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 440x
            Sequencing Technology             :: Oxford Nanopore MinION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 08/21/2023 17:24:28
            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)                     :: 5,696
            CDSs (total)                      :: 5,563
            Genes (coding)                    :: 5,398
            CDSs (with protein)               :: 5,398
            Genes (RNA)                       :: 133
            rRNAs                             :: 9, 8, 8 (5S, 16S, 23S)
            complete rRNAs                    :: 9, 8, 8 (5S, 16S, 23S)
            tRNAs                             :: 90
            ncRNAs                            :: 18
            Pseudo Genes (total)              :: 165
            CDSs (without protein)            :: 165
            Pseudo Genes (ambiguous residues) :: 0 of 165
            Pseudo Genes (frameshifted)       :: 66 of 165
            Pseudo Genes (incomplete)         :: 102 of 165
            Pseudo Genes (internal stop)      :: 30 of 165
            Pseudo Genes (multiple problems)  :: 30 of 165
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP132644.1.
            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..6141
                     /organism="Klebsiella pneumoniae"
                     /mol_type="genomic DNA"
                     /strain="589376"
                     /isolation_source="respiratory"
                     /host="Homo sapiens"
                     /db_xref="taxon:573"
                     /plasmid="p6"
                     /geo_loc_name="Afghanistan:Bagram"
                     /collection_date="2018-07-15"
                     /collected_by="Multidrug Resistance Surveillance Network"
     gene            join(6036..6141,1..287)
                     /locus_tag="QRD00_RS28450"
                     /old_locus_tag="QRD00_28430"
     CDS             join(6036..6141,1..287)
                     /locus_tag="QRD00_RS28450"
                     /old_locus_tag="QRD00_28430"
                     /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="antitoxin VbhA family protein"
                     /protein_id="WP_043907050.1"
                     /translation="MSTTQIEKDSRRKAVNGVISSFQLEGEAITDEFKILLEDYINGKI
                     STDEVLAMVSDEPTTTEYDYEITPRTLGLGGGWNLRLLENGEEVGGGVFPLPEHCDFRD
                     EKALQTLLDSLYEDALAEASAWLASR"
                     /name="antitoxin VbhA family protein"
     gene            269..607
                     /locus_tag="QRD00_RS28455"
                     /old_locus_tag="QRD00_28435"
     CDS             269..607
                     /locus_tag="QRD00_RS28455"
                     /old_locus_tag="QRD00_28435"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000502641.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MobC family plasmid mobilization relaxosome
                     protein"
                     /protein_id="WP_043907051.1"
                     /translation="MAGQPLKRLRSIKIRVSDAELERLRELCPKAQLAEWMREQCLGVA
                     QPQRRTPAPTVDPALLRQLAGMGNNLNQIARRVNSGEWGPLDRLRIIAELSAIGRELEE
                     LHHDHQIP"
                     /name="MobC family plasmid mobilization relaxosome protein"
     gene            588..2042
                     /locus_tag="QRD00_RS28460"
                     /old_locus_tag="QRD00_28440"
     CDS             588..2042
                     /locus_tag="QRD00_RS28460"
                     /old_locus_tag="QRD00_28440"
                     /inference="COORDINATES: protein motif:HMM:NF015397.3"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="relaxase/mobilization nuclease domain-containing
                     protein"
                     /protein_id="WP_064996073.1"
                     /translation="MIIKFHNRGVGRGSGPVGYLLGRDGNREGATLDRGNPAVIEALID
                     SSPYAKKYTSGVLSFAEADLPRATKDKLMSDFEKALLPGLEGNQYAVLWVEHRDKGRLE
                     LNFVVPNIELQSGKRLQPYFHKADNPRLDAWRTVVNGELKLHDPDDPLNRQAVITPKDL
                     PRGHKEAAQAITDGLLRMAGAGEIQSRDDVRKALQGAGFSVVRETKNSLSIADPDGGRN
                     IRLKGVLYEQDFRHGEGLRAELEAAGQRYREASDRRIHEARESYLRGVEIKRGENERRY
                     CRAQPENGLAVAQNVDLDAGQHRPVLERNERDPLVSGGIDSGAASHSPSLGREGRQAKA
                     DPVREEIGAPLRADLRPQSNRLGEGYLLDRAEGVLNDGIGAGIALRVRGFAERIRAAAQ
                     GMAGKLRELGEHVREHQTRGRDQQGSSRAIDEAGERLNAASGRLEQAAGGLDRASQQVA
                     KEREHRLLKALDRGWERGDRSRGFER"
                     /name="relaxase/mobilization nuclease domain-containing
                     protein"
     gene            complement(2324..2605)
                     /locus_tag="QRD00_RS28465"
                     /old_locus_tag="QRD00_28445"
     CDS             complement(2324..2605)
                     /locus_tag="QRD00_RS28465"
                     /old_locus_tag="QRD00_28445"
                     /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_043907053.1"
                     /translation="MGFFNLSKALEEVSDAFGAKETAIASAKLLGKGVVNLAHFAATTG
                     LDSVVKQTSNKVLNSESSTEEQREQAKKSAAWADARIAARNKAENTED"
                     /name="hypothetical protein"
     gene            2949..3746
                     /locus_tag="QRD00_RS28470"
                     /old_locus_tag="QRD00_28450"
     CDS             2949..3746
                     /locus_tag="QRD00_RS28470"
                     /old_locus_tag="QRD00_28450"
                     /EC_number="3.5.2.6"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_011071128.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="OXA-48 family carbapenem-hydrolyzing class D
                     beta-lactamase OXA-232"
                     /protein_id="WP_043907054.1"
                     /translation="MRVLALSAVFLVASIIGMPAVAKEWQENKSWNAHFTEHKSQGVVV
                     LWNENKQQGFTNNLKRANQAFLPASTFKIPNSLIALDLGVVKDEHQVFKWDGQTRDIAA
                     WNRDHDLITAMKYSVVPVYQEFARQIGEARMSKMLHAFDYGNEDISGNVDSFWLDGGIR
                     ISATQQIAFLRKLYHNKLHVSERSQRIVKQAMLTEANGDYIIRAKTGYSTSIEPKIGWW
                     VGWVELDDNVWFFAMNMDMPTSDGLGLRQAITKEVLKQEKIIP"
                     /name="OXA-48 family carbapenem-hydrolyzing class D
                     beta-lactamase OXA-232"
     gene            complement(4153..>4305)
                     /locus_tag="QRD00_RS28475"
                     /old_locus_tag="QRD00_28455"
                     /pseudo=""
     CDS             complement(4153..>4305)
                     /locus_tag="QRD00_RS28475"
                     /old_locus_tag="QRD00_28455"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_015059985.1"
                     /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="EreA family erythromycin esterase"
                     /name="EreA family erythromycin esterase"
     gene            4681..5628
                     /locus_tag="QRD00_RS28480"
                     /old_locus_tag="QRD00_28460"
     CDS             4681..5628
                     /locus_tag="QRD00_RS28480"
                     /old_locus_tag="QRD00_28460"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_014293673.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="replication initiation protein"
                     /protein_id="WP_015060053.1"
                     /translation="MRKCAQLELFRERLPRKPYYSDELTTGLRIADVARALGARYIQPN
                     GPTHRHWIVFDVDHAAATLSWDDVGAPAPNITVTNKANGHAHLIYGLDTPIRTAPDGNA
                     APLRYAAAIEAALREKLGADMGYSGLICKNPLHEHWLVQVWEPRLYDLAWLSDYLDLSS
                     YNGRKSLPEYGLGRNCTLFEKTRLWAYKAIRQGWPDYPEWLAACVDRASGYNAQFEQPL
                     PANEVRHTAKSIAKWTHQHLSPAGFREEQARRGAKGGKVSKGGGRPSNSGKDKSDLLPE
                     VLRLKAQGYTNRDIADDLQISPSTVSVYLKRDRP"
                     /name="replication initiation protein"
     ARG             2950..3743
                     /name="blaOXA-232"
                     /gene="blaOXA-232"
                     /gene_name="OXA-48 family carbapenem-hydrolyzing class D
                     beta-lactamase OXA-232"
                     /tool="amrfinderplus"
                     /drug_class="BETA-LACTAM"
                     /identity="100.0"
                     /coverage="100.0"
     Typing          4694..5615
                     /name="rep_cluster_1195"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="81.974"
                     /coverage="98.0"
                     /evalue="0.0"
     Typing          589..2039
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="98.554"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 tacttgaaga ttatatcaat ggaaaaattt ccaccgatga ggtgttagct atggtaagtg
       61 acgaacccac aacaacggaa tacgactacg aaatcacccc ccgcactctc ggtcttggcg
      121 ggggctggaa tctgcgtttg ctggagaacg gcgaagaggt cggcgggggt gttttcccct
      181 tgccggagca ctgcgatttt cgggatgaaa aggcgctcca gacgctactc gatagcctct
      241 atgaggacgc cttagcggag gcctctgcat ggctggccag ccgttaaagc gcctccgctc
      301 tatcaagatc cgggtctcag atgcggagct tgagcgcctg cgggagctct gccccaaggc
      361 ccaactggcg gagtggatgc gggagcaatg tctcggtgtt gcgcaacccc agcgccgaac
      421 gccggcgcct accgtagatc cggcgctctt gcggcagttg gccggaatgg gcaacaacct
      481 gaaccagatc gcccggcgcg ttaattccgg ggagtggggg ccgttggatc ggctgcgcat
      541 catagcggag ctgtccgcta taggccgcga gctggaggaa ctgcaccatg atcatcaaat
      601 tccataaccg tggggtaggc cggggctccg ggcctgttgg ctacttgttg ggccgtgacg
      661 ggaaccggga aggcgcaacg ctcgaccggg gcaaccctgc ggtgattgaa gccctgattg
      721 attccagtcc ctacgccaaa aaatacacct ctggcgttct gtcgtttgcc gaggctgatt
      781 tacccagggc gaccaaggac aagctgatga gcgactttga aaaggcgctc ctgcccggac
      841 tggagggcaa ccagtacgct gttttgtggg tagagcaccg cgacaagggg cggctggagc
      901 tgaattttgt agtcccgaac atcgaattgc agagcgggaa gcggctgcaa ccctacttcc
      961 acaaggccga caatccgcgc ctcgatgcgt ggcgaaccgt ggtaaacggg gagctgaaat
     1021 tgcacgaccc ggacgatccg ttaaaccgtc aggccgttat cacgccaaag gatttgccga
     1081 gggggcacaa ggaggccgct caggccatta cagacgggct tttacgcatg gccggagcag
     1141 gggagatcca gagccgcgat gatgtgcgca aagccttgca gggtgcgggt ttcagcgtgg
     1201 tacgcgaaac caaaaacagc ctgagcattg ccgacccgga cggggggcgg aacatccgat
     1261 taaagggggt gctgtatgag caagatttta gacatggcga aggacttcga gcagagctcg
     1321 aagcagcagg ccaacgctat cgagaagcgt ctgaccgaag aattcacgag gcacgagaaa
     1381 gctatctccg gggcgttgaa atcaagcgag gagaaaatga gcgccgctat tgccgagcac
     1441 agccagaaaa tgggctggct gttgctcaaa acgtggatct ggatgctggt cagcatcgtc
     1501 ctgttcttga gcgcaacgag cgggatcctc tggtatcagg gggaattgat agcggagcgg
     1561 caagccactc tccaagcctt ggcagagaag ggcggcaagc taaagctgac ccagtgcggg
     1621 aagaaattgg agcacctttg cgtgcagatc tccgacccca atccaaccgt ttgggggaag
     1681 gatacctatt ggatcgtgcc gaaggggtac taaatgacgg gattggagcg ggaattgctc
     1741 tgcgcgttcg aggctttgca gagcgcatac gagcagcagc acaaggcatg gcaggaaagc
     1801 tacgcgaact tggcgagcat gtacgagagc accaaacaag aggccgagat cagcagggca
     1861 gcagcagagc gattgacgag gcaggtgaac ggcttaacgc agcaagtgga cggcttgagc
     1921 aagcagctgg agggcttgac cgggctagtc agcaagttgc aaaagaaagg gaacacaggc
     1981 tcctgaaggc actggatcga ggctgggagc gtggagacag atcgcgaggc tttgagcgtt
     2041 gacggaacaa aacggccgtc agttataaaa aaaggaaagt gctatcactt tccttttatc
     2101 ggcgggaatt atcgttgagt tcttctatgc catttttcat agtagtaact gtaatcttca
     2161 tctctaccac cagattcaat ccagtcatca tactcagggc tatttttgaa atctgaatca
     2221 gacatgctaa ctccttgtta ttagttggct tctatggaag ctagcgcacc gtgaagttat
     2281 gatcaacgat gtagtccaca tcattgtcga aatgtgcgtt cagctagtct tcggtgtttt
     2341 ctgctttatt tctagcggcg attctcgcgt ctgcccatgc ggcagacttt ttagcctgtt
     2401 ctcgttgttc ttcggttgaa gactcgctgt tgagaacttt gttgctcgtt tgtttgacca
     2461 ccgaatccaa acctgttgtt gctgcaaaat gagctaggtt aacaactccc ttacctaaca
     2521 acttggcact agcgattgcg gtttctttag ccccaaaagc atcagacacc tcctcaagcg
     2581 ctttagatag gttaaaaaat cccatactcc ccctaagaat atcatcaata aaattgagtg
     2641 ttgctctgtg gataacttgc agagtttatt aagtatcatt gcagcaaaga tgaaatcaat
     2701 gatttatcaa aaatgattga aaggtggttg taaataatgt tacaatgtgt gagaagcagt
     2761 ctaaattctt cgtgaaatag tgatttttga agctaataaa aaacacacgt ggaatttagg
     2821 taatagttaa agcttgtgcc tgattgttgc cacaattggt cagcagtttg ctagggaatg
     2881 agagggcaga gaatgataag cttagcactt aatttgtatg gatatattgc attaagcaag
     2941 gggacgttat gcgtgtatta gccttatcgg ctgtgttttt ggtggcatcg attatcggaa
     3001 tgccagcggt agcaaaggaa tggcaagaaa acaaaagttg gaatgctcac tttactgaac
     3061 ataaatcaca gggcgtagtt gtgctctgga atgagaataa gcagcaagga tttaccaata
     3121 atcttaaacg ggcgaaccaa gcatttttac ccgcatctac ctttaaaatt cccaatagct
     3181 tgatcgccct cgatttgggc gtggttaagg atgaacacca agtctttaag tgggatggac
     3241 agacgcgtga tatcgccgct tggaatcgtg accatgactt aattaccgcg atgaagtact
     3301 cagttgtgcc tgtttatcaa gaatttgccc gccaaattgg tgaggcacgt atgagtaaaa
     3361 tgctgcacgc cttcgattat ggcaatgagg atatctcggg caatgtagac agtttttggc
     3421 tcgatggtgg tattcgcatt tcggctaccc agcaaatcgc ttttttacgc aagctgtatc
     3481 acaacaagct gcacgtttct gagcgtagtc agcgcatcgt gaaacaagcc atgctgaccg
     3541 aagccaatgg cgactatatt attcgggcta aaacgggata ctcgactagt atcgaaccta
     3601 agattggctg gtgggttggt tgggttgaac ttgatgataa tgtgtggttt tttgcgatga
     3661 atatggatat gcccacatcg gatggtttag ggctgcgcca agccatcaca aaagaagtgc
     3721 tcaaacagga gaaaattatt ccctagaagt ggttagcgcg tatttgtgtg aaatagccgt
     3781 catataagct gtaaagatat atggacaaaa tgctgatgct cgatgcgctt gtagttaatg
     3841 gctcatactt aatcggtcag gcctaatcga cttaagctcc gcgcgttaac tttcagcctg
     3901 agcattagca tcacattcct aaacgtaaaa agcctagcca atttgctagg cttttttgtt
     3961 atctcaatgg ccatggtcac tcaacatggg ggtgtgaata aaggagtggc gatgtcagta
     4021 aaggtgaatg ccgctgcgat aaagtgccta gcccatcaag gattgtaggc tttcttggct
     4081 gctaaagcgt ttgacgaaaa agtccaagaa ggcgctgata ttggttctcc atcattttca
     4141 tctaccggtt tactataggt caaccaggcc gtccttgccg gcgcttggga cgcagacgat
     4201 ggcatcaaat gcctcgctca aattcgtttc tacagaggcg ctttgggacc gcattcgctt
     4261 tgctttcatg ggggcatctg tcaatgtcag acatgaatcc tccgatatag gttgattttt
     4321 gatctcttca acacttggtg ttgtccgact agagagactt atatggatca gtattcttgc
     4381 actgacaatg gtgccactca atcccaagga tcgacctagt tagaggcgta gatcaagcaa
     4441 ttcaaaacag cgcagaagca gaaggaggtg gaaatatgtt ccagggtgaa aggttacatg
     4501 caactaacgt tgctctctag gatgtgcctg ctgtaacgta ttgtccagaa aagacaaacc
     4561 cccgttatcg cttgcatctt ggcggagctg cgaaaaacgg gggccgtgac gaatcacaag
     4621 agaagtctat cacatggatc atgccaaaca accccacgcc gccaataagc gcggtggtgc
     4681 ttgagaaagt gcgcacagct tgagctgttt cgggagcgcc tgccccggaa accctactat
     4741 tccgacgagc ttacaacggg cctacggatt gcggatgttg cccgcgccct tggtgcgcgt
     4801 tacatccagc cgaacgggcc aacgcaccgc cactggatcg tttttgacgt agaccatgca
     4861 gccgctacgt tatcttggga tgacgtaggc gctccagccc ctaacattac cgtcacgaac
     4921 aaggccaacg gccacgcgca tctgatctac ggactggata cgccgatccg cactgccccg
     4981 gatggaaatg cagcccctct gcggtatgcc gccgccatcg aggccgcgct ccgggagaaa
     5041 ttaggggcgg atatgggcta ctccgggctg atctgcaaga accccctgca tgagcactgg
     5101 ctggtgcagg tatgggaacc ccggctctac gatttagcct ggctatccga ttacctcgat
     5161 ctgagctcct acaatggccg caaatcgctt cctgagtacg ggcttgggcg aaactgtacc
     5221 ctgttcgaga aaacgcgcct gtgggcctat aaagcgatcc ggcagggctg gccggattac
     5281 cccgaatggt tggccgcttg tgttgaccgg gcatcaggat ataacgccca gttcgagcag
     5341 ccgctccccg caaacgaagt ccggcacacg gccaagtcca ttgccaaatg gacgcaccag
     5401 cacctaagcc ccgcagggtt cagagaggag caggcccgga gaggtgcgaa gggcggcaag
     5461 gtatccaagg gagggggaag gccgagcaat agcggtaagg acaagtccga tctattgccg
     5521 gaggttctgc ggcttaaggc tcaggggtac accaaccgcg atatagcgga cgatcttcaa
     5581 atctccccca gtacggtgag cgtttaccta aagcgtgatc gtccgtgatc gaaacaagcc
     5641 ttatcagata atagccccct ttaggggggt tcctgcgctc ttgtctttta gccttaaaaa
     5701 atccttttag cgcggatctt tggcgaggtg gacaactgcg cctgtccgtc catcgccccc
     5761 ctgttttttc ggggggtgtg ggcggcagca gttatccacg gagccgctct ttcccttgat
     5821 cttgctctag ggcttgcagt atcccgccca tggttgaata atgtactaag caaggctaca
     5881 cagaggcccc tctacctgct tcgcggtctc gggcctctgt ggccttgttc aggggtgcta
     5941 cgcccccccg aaaccccctg tggcccccgc tcgatccgcc ccttcgggac ggtctgcgcg
     6001 gtggcttctt ggctctggag aatggacgag gccctatgtc aacaacacag atagagaaag
     6061 attcgagaag gaaggcagtc aatggcgtta tttctagttt ccaactagag ggggaggcca
     6121 taaccgatga attcaaaatt c
//
