LOCUS       NZ_CP135483             6141 bp    DNA     circular CON 07-OCT-2023
DEFINITION  Klebsiella pneumoniae strain isolateE plasmid pIsolateE_B, complete
            sequence.
ACCESSION   NZ_CP135483
VERSION     NZ_CP135483.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN37529176
            Assembly: GCF_032348595.1
KEYWORDS    RefSeq.
SOURCE      Klebsiella pneumoniae
  ORGANISM  Klebsiella pneumoniae
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Klebsiella/Raoultella group; Klebsiella.
REFERENCE   1  (bases 1 to 6141)
  AUTHORS   Lerminiaux,N., Fakharuddin,K., Mulvey,M.R. and Mataseje,L.
  TITLE     Do we still need Illumina sequencing data?: Evaluating Oxford
            Nanopore Technologies R10.4.1 flow cells and v14 library prep kits
            for Gram negative bacteria whole genome assemblies
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 6141)
  AUTHORS   Lerminiaux,N., Fakharuddin,K., Mulvey,M.R. and Mataseje,L.
  TITLE     Direct Submission
  JOURNAL   Submitted (25-SEP-2023) National Microbiology Lab, Public Health
            Agency of Canada, 1015 Arlington Street, Winnipeg R3E3R2, Canada
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Date                     :: 21-JUN-2023
            Assembly Method :: Trycycler v. v0.5.0; Flye v. v2.9.2; Raven v.
            v1.8.1; Miniasm/minipolish v. v0.3_r179
            Assembly Name                     :: isolateE
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 171X
            Sequencing Technology :: Oxford Nanopore MinION; Illumina MiSeq
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 10/07/2023 13:44:41
            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)                     :: 5,389
            CDSs (total)                      :: 5,265
            Genes (coding)                    :: 5,165
            CDSs (with protein)               :: 5,165
            Genes (RNA)                       :: 124
            rRNAs                             :: 9, 8, 8 (5S, 16S, 23S)
            complete rRNAs                    :: 9, 8, 8 (5S, 16S, 23S)
            tRNAs                             :: 86
            ncRNAs                            :: 13
            Pseudo Genes (total)              :: 100
            CDSs (without protein)            :: 100
            Pseudo Genes (ambiguous residues) :: 0 of 100
            Pseudo Genes (frameshifted)       :: 47 of 100
            Pseudo Genes (incomplete)         :: 60 of 100
            Pseudo Genes (internal stop)      :: 14 of 100
            Pseudo Genes (multiple problems)  :: 20 of 100
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP135483.1.
            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="isolateE"
                     /host="Homo sapiens"
                     /db_xref="taxon:573"
                     /plasmid="pIsolateE_B"
                     /geo_loc_name="Canada: Ottawa"
                     /collection_date="2021"
     gene            290..1237
                     /locus_tag="RRL12_RS26790"
                     /old_locus_tag="RRL12_26790"
     CDS             290..1237
                     /locus_tag="RRL12_RS26790"
                     /old_locus_tag="RRL12_26790"
                     /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"
     gene            1645..2037
                     /locus_tag="RRL12_RS26795"
                     /old_locus_tag="RRL12_26795"
     CDS             1645..2037
                     /locus_tag="RRL12_RS26795"
                     /old_locus_tag="RRL12_26795"
                     /inference="COORDINATES: protein motif:HMM:NF037437.3"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /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            2019..2357
                     /locus_tag="RRL12_RS26800"
                     /old_locus_tag="RRL12_26800"
     CDS             2019..2357
                     /locus_tag="RRL12_RS26800"
                     /old_locus_tag="RRL12_26800"
                     /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            2338..3792
                     /locus_tag="RRL12_RS26805"
                     /old_locus_tag="RRL12_26805"
     CDS             2338..3792
                     /locus_tag="RRL12_RS26805"
                     /old_locus_tag="RRL12_26805"
                     /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(4074..4355)
                     /locus_tag="RRL12_RS26810"
                     /old_locus_tag="RRL12_26810"
     CDS             complement(4074..4355)
                     /locus_tag="RRL12_RS26810"
                     /old_locus_tag="RRL12_26810"
                     /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            4699..5496
                     /locus_tag="RRL12_RS26815"
                     /old_locus_tag="RRL12_26815"
     CDS             4699..5496
                     /locus_tag="RRL12_RS26815"
                     /old_locus_tag="RRL12_26815"
                     /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(5903..>6055)
                     /locus_tag="RRL12_RS26820"
                     /old_locus_tag="RRL12_26820"
                     /pseudo=""
     CDS             complement(5903..>6055)
                     /locus_tag="RRL12_RS26820"
                     /old_locus_tag="RRL12_26820"
                     /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"
     ARG             4700..5493
                     /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          303..1224
                     /name="rep_cluster_1195"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="81.974"
                     /coverage="98.0"
                     /evalue="0.0"
     Typing          2339..3789
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="98.554"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 tgccactcaa tcccaaggat cgacctagtt agaggcgtag atcaagcaat tcaaaacagc
       61 gcagaagcag aaggaggtgg aaatatgttc cagggtgaaa ggttacatgc aactaacgtt
      121 gctctctagg atgtgcctgc tgtaacgtat tgtccagaaa agacaaaccc ccgttatcgc
      181 ttgcatcttg gcggagctgc gaaaaacggg ggccgtgacg aatcacaaga gaagtctatc
      241 acatggatca tgccaaacaa ccccacgccg ccaataagcg cggtggtgct tgagaaagtg
      301 cgcacagctt gagctgtttc gggagcgcct gccccggaaa ccctactatt ccgacgagct
      361 tacaacgggc ctacggattg cggatgttgc ccgcgccctt ggtgcgcgtt acatccagcc
      421 gaacgggcca acgcaccgcc actggatcgt ttttgacgta gaccatgcag ccgctacgtt
      481 atcttgggat gacgtaggcg ctccagcccc taacattacc gtcacgaaca aggccaacgg
      541 ccacgcgcat ctgatctacg gactggatac gccgatccgc actgccccgg atggaaatgc
      601 agcccctctg cggtatgccg ccgccatcga ggccgcgctc cgggagaaat taggggcgga
      661 tatgggctac tccgggctga tctgcaagaa ccccctgcat gagcactggc tggtgcaggt
      721 atgggaaccc cggctctacg atttagcctg gctatccgat tacctcgatc tgagctccta
      781 caatggccgc aaatcgcttc ctgagtacgg gcttgggcga aactgtaccc tgttcgagaa
      841 aacgcgcctg tgggcctata aagcgatccg gcagggctgg ccggattacc ccgaatggtt
      901 ggccgcttgt gttgaccggg catcaggata taacgcccag ttcgagcagc cgctccccgc
      961 aaacgaagtc cggcacacgg ccaagtccat tgccaaatgg acgcaccagc acctaagccc
     1021 cgcagggttc agagaggagc aggcccggag aggtgcgaag ggcggcaagg tatccaaggg
     1081 agggggaagg ccgagcaata gcggtaagga caagtccgat ctattgccgg aggttctgcg
     1141 gcttaaggct caggggtaca ccaaccgcga tatagcggac gatcttcaaa tctcccccag
     1201 tacggtgagc gtttacctaa agcgtgatcg tccgtgatcg aaacaagcct tatcagataa
     1261 tagccccctt taggggggtt cctgcgctct tgtcttttag ccttaaaaaa tccttttagc
     1321 gcggatcttt ggcgaggtgg acaactgcgc ctgtccgtcc atcgcccccc tgttttttcg
     1381 gggggtgtgg gcggcagcag ttatccacgg agccgctctt tcccttgatc ttgctctagg
     1441 gcttgcagta tcccgcccat ggttgaataa tgtactaagc aaggctacac agaggcccct
     1501 ctacctgctt cgcggtctcg ggcctctgtg gccttgttca ggggtgctac gcccccccga
     1561 aaccccctgt ggcccccgct cgatccgccc cttcgggacg gtctgcgcgg tggcttcttg
     1621 gctctggaga atggacgagg ccctatgtca acaacacaga tagagaaaga ttcgagaagg
     1681 aaggcagtca atggcgttat ttctagtttc caactagagg gggaggccat aaccgatgaa
     1741 ttcaaaattc tacttgaaga ttatatcaat ggaaaaattt ccaccgatga ggtgttagct
     1801 atggtaagtg acgaacccac aacaacggaa tacgactacg aaatcacccc ccgcactctc
     1861 ggtcttggcg ggggctggaa tctgcgtttg ctggagaacg gcgaagaggt cggcgggggt
     1921 gttttcccct tgccggagca ctgcgatttt cgggatgaaa aggcgctcca gacgctactc
     1981 gatagcctct atgaggacgc cttagcggag gcctctgcat ggctggccag ccgttaaagc
     2041 gcctccgctc tatcaagatc cgggtctcag atgcggagct tgagcgcctg cgggagctct
     2101 gccccaaggc ccaactggcg gagtggatgc gggagcaatg tctcggtgtt gcgcaacccc
     2161 agcgccgaac gccggcgcct accgtagatc cggcgctctt gcggcagttg gccggaatgg
     2221 gcaacaacct gaaccagatc gcccggcgcg ttaattccgg ggagtggggg ccgttggatc
     2281 ggctgcgcat catagcggag ctgtccgcta taggccgcga gctggaggaa ctgcaccatg
     2341 atcatcaaat tccataaccg tggggtaggc cggggctccg ggcctgttgg ctacttgttg
     2401 ggccgtgacg ggaaccggga aggcgcaacg ctcgaccggg gcaaccctgc ggtgattgaa
     2461 gccctgattg attccagtcc ctacgccaaa aaatacacct ctggcgttct gtcgtttgcc
     2521 gaggctgatt tacccagggc gaccaaggac aagctgatga gcgactttga aaaggcgctc
     2581 ctgcccggac tggagggcaa ccagtacgct gttttgtggg tagagcaccg cgacaagggg
     2641 cggctggagc tgaattttgt agtcccgaac atcgaattgc agagcgggaa gcggctgcaa
     2701 ccctacttcc acaaggccga caatccgcgc ctcgatgcgt ggcgaaccgt ggtaaacggg
     2761 gagctgaaat tgcacgaccc ggacgatccg ttaaaccgtc aggccgttat cacgccaaag
     2821 gatttgccga gggggcacaa ggaggccgct caggccatta cagacgggct tttacgcatg
     2881 gccggagcag gggagatcca gagccgcgat gatgtgcgca aagccttgca gggtgcgggt
     2941 ttcagcgtgg tacgcgaaac caaaaacagc ctgagcattg ccgacccgga cggggggcgg
     3001 aacatccgat taaagggggt gctgtatgag caagatttta gacatggcga aggacttcga
     3061 gcagagctcg aagcagcagg ccaacgctat cgagaagcgt ctgaccgaag aattcacgag
     3121 gcacgagaaa gctatctccg gggcgttgaa atcaagcgag gagaaaatga gcgccgctat
     3181 tgccgagcac agccagaaaa tgggctggct gttgctcaaa acgtggatct ggatgctggt
     3241 cagcatcgtc ctgttcttga gcgcaacgag cgggatcctc tggtatcagg gggaattgat
     3301 agcggagcgg caagccactc tccaagcctt ggcagagaag ggcggcaagc taaagctgac
     3361 ccagtgcggg aagaaattgg agcacctttg cgtgcagatc tccgacccca atccaaccgt
     3421 ttgggggaag gatacctatt ggatcgtgcc gaaggggtac taaatgacgg gattggagcg
     3481 ggaattgctc tgcgcgttcg aggctttgca gagcgcatac gagcagcagc acaaggcatg
     3541 gcaggaaagc tacgcgaact tggcgagcat gtacgagagc accaaacaag aggccgagat
     3601 cagcagggca gcagcagagc gattgacgag gcaggtgaac ggcttaacgc agcaagtgga
     3661 cggcttgagc aagcagctgg agggcttgac cgggctagtc agcaagttgc aaaagaaagg
     3721 gaacacaggc tcctgaaggc actggatcga ggctgggagc gtggagacag atcgcgaggc
     3781 tttgagcgtt gacggaacaa aacggccgtc agttataaaa aaaggaaagt gctatcactt
     3841 tccttttatc ggcgggaatt atcgttgagt tcttctatgc catttttcat agtagtaact
     3901 gtaatcttca tctctaccac cagattcaat ccagtcatca tactcagggc tatttttgaa
     3961 atctgaatca gacatgctaa ctccttgtta ttagttggct tctatggaag ctagcgcacc
     4021 gtgaagttat gatcaacgat gtagtccaca tcattgtcga aatgtgcgtt cagctagtct
     4081 tcggtgtttt ctgctttatt tctagcggcg attctcgcgt ctgcccatgc ggcagacttt
     4141 ttagcctgtt ctcgttgttc ttcggttgaa gactcgctgt tgagaacttt gttgctcgtt
     4201 tgtttgacca ccgaatccaa acctgttgtt gctgcaaaat gagctaggtt aacaactccc
     4261 ttacctaaca acttggcact agcgattgcg gtttctttag ccccaaaagc atcagacacc
     4321 tcctcaagcg ctttagatag gttaaaaaat cccatactcc ccctaagaat atcatcaata
     4381 aaattgagtg ttgctctgtg gataacttgc agagtttatt aagtatcatt gcagcaaaga
     4441 tgaaatcaat gatttatcaa aaatgattga aaggtggttg taaataatgt tacaatgtgt
     4501 gagaagcagt ctaaattctt cgtgaaatag tgatttttga agctaataaa aaacacacgt
     4561 ggaatttagg taatagttaa agcttgtgcc tgattgttgc cacaattggt cagcagtttg
     4621 ctagggaatg agagggcaga gaatgataag cttagcactt aatttgtatg gatatattgc
     4681 attaagcaag gggacgttat gcgtgtatta gccttatcgg ctgtgttttt ggtggcatcg
     4741 attatcggaa tgccagcggt agcaaaggaa tggcaagaaa acaaaagttg gaatgctcac
     4801 tttactgaac ataaatcaca gggcgtagtt gtgctctgga atgagaataa gcagcaagga
     4861 tttaccaata atcttaaacg ggcgaaccaa gcatttttac ccgcatctac ctttaaaatt
     4921 cccaatagct tgatcgccct cgatttgggc gtggttaagg atgaacacca agtctttaag
     4981 tgggatggac agacgcgtga tatcgccgct tggaatcgtg accatgactt aattaccgcg
     5041 atgaagtact cagttgtgcc tgtttatcaa gaatttgccc gccaaattgg tgaggcacgt
     5101 atgagtaaaa tgctgcacgc cttcgattat ggcaatgagg atatctcggg caatgtagac
     5161 agtttttggc tcgatggtgg tattcgcatt tcggctaccc agcaaatcgc ttttttacgc
     5221 aagctgtatc acaacaagct gcacgtttct gagcgtagtc agcgcatcgt gaaacaagcc
     5281 atgctgaccg aagccaatgg cgactatatt attcgggcta aaacgggata ctcgactagt
     5341 atcgaaccta agattggctg gtgggttggt tgggttgaac ttgatgataa tgtgtggttt
     5401 tttgcgatga atatggatat gcccacatcg gatggtttag ggctgcgcca agccatcaca
     5461 aaagaagtgc tcaaacagga gaaaattatt ccctagaagt ggttagcgcg tatttgtgtg
     5521 aaatagccgt catataagct gtaaagatat atggacaaaa tgctgatgct cgatgcgctt
     5581 gtagttaatg gctcatactt aatcggtcag gcctaatcga cttaagctcc gcgcgttaac
     5641 tttcagcctg agcattagca tcacattcct aaacgtaaaa agcctagcca atttgctagg
     5701 cttttttgtt atctcaatgg ccatggtcac tcaacatggg ggtgtgaata aaggagtggc
     5761 gatgtcagta aaggtgaatg ccgctgcgat aaagtgccta gcccatcaag gattgtaggc
     5821 tttcttggct gctaaagcgt ttgacgaaaa agtccaagaa ggcgctgata ttggttctcc
     5881 atcattttca tctaccggtt tactataggt caaccaggcc gtccttgccg gcgcttggga
     5941 cgcagacgat ggcatcaaat gcctcgctca aattcgtttc tacagaggcg ctttgggacc
     6001 gcattcgctt tgctttcatg ggggcatctg tcaatgtcag acatgaatcc tccgatatag
     6061 gttgattttt gatctcttca acacttggtg ttgtccgact agagagactt atatggatca
     6121 gtattcttgc actgacaatg g
//
