LOCUS       NZ_CP135511             4168 bp    DNA     circular CON 07-OCT-2023
DEFINITION  Klebsiella pneumoniae strain isolateK plasmid pIsolateK_C, complete
            sequence.
ACCESSION   NZ_CP135511
VERSION     NZ_CP135511.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN37529182
            Assembly: GCF_032343715.1
KEYWORDS    RefSeq.
SOURCE      Klebsiella pneumoniae
  ORGANISM  Klebsiella pneumoniae
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Klebsiella/Raoultella group; Klebsiella.
REFERENCE   1  (bases 1 to 4168)
  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  JOURNAL   Unpublished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 4168)
  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                     :: isolateK
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 229X
            Sequencing Technology :: Oxford Nanopore MinION; Illumina MiSeq
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 10/07/2023 13:32:04
            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)                     :: 5,641
            CDSs (total)                      :: 5,515
            Genes (coding)                    :: 5,398
            CDSs (with protein)               :: 5,398
            Genes (RNA)                       :: 126
            rRNAs                             :: 9, 8, 8 (5S, 16S, 23S)
            complete rRNAs                    :: 9, 8, 8 (5S, 16S, 23S)
            tRNAs                             :: 87
            ncRNAs                            :: 14
            Pseudo Genes (total)              :: 117
            CDSs (without protein)            :: 117
            Pseudo Genes (ambiguous residues) :: 0 of 117
            Pseudo Genes (frameshifted)       :: 42 of 117
            Pseudo Genes (incomplete)         :: 73 of 117
            Pseudo Genes (internal stop)      :: 20 of 117
            Pseudo Genes (multiple problems)  :: 15 of 117
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP135511.1.
            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..4168
                     /organism="Klebsiella pneumoniae"
                     /mol_type="genomic DNA"
                     /strain="isolateK"
                     /host="Homo sapiens"
                     /db_xref="taxon:573"
                     /plasmid="pIsolateK_C"
                     /geo_loc_name="Canada: Ottawa"
                     /collection_date="2020"
     gene            226..417
                     /locus_tag="RRL08_RS28140"
                     /old_locus_tag="RRL08_28140"
     CDS             226..417
                     /locus_tag="RRL08_RS28140"
                     /old_locus_tag="RRL08_28140"
                     /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="WP_004187666.1"
                     /translation="MTKQQKTALNMAKFIQNQSLLLLEKLNELDLDVEADLCEKLHDDA
                     EHLFRTLSSRLDALQDGN"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            417..818
                     /locus_tag="RRL08_RS28145"
                     /old_locus_tag="RRL08_28145"
     CDS             417..818
                     /locus_tag="RRL08_RS28145"
                     /old_locus_tag="RRL08_28145"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_009310048.1"
                     /GO_function="GO:0003677 - DNA binding [Evidence IEA]"
                     /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="WP_012579088.1"
                     /translation="MARVSISEAARLTGKSRTTLHRLIKAGDLSTCSGERNAKMVDTSE
                     LLRVFGPFEQPKGEHHSGQVSGQRDTASADQSEQVIRHLKQEIEHLNTLLLSKDSHIDS
                     LKQAMLLLENHQAKLTESPAPWWKFWKKS"
                     /name="helix-turn-helix domain-containing protein"
     gene            complement(1773..2405)
                     /locus_tag="RRL08_RS28150"
                     /old_locus_tag="RRL08_28150"
     CDS             complement(1773..2405)
                     /locus_tag="RRL08_RS28150"
                     /old_locus_tag="RRL08_28150"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000804504.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="DUF3226 domain-containing protein"
                     /protein_id="WP_012579086.1"
                     /translation="MKDINNSKKIIFVEGDDDFHFLCNLLEIQGITDVFVEKINGKSKL
                     KQALRAFKNIDSFDEKESIFIILDADTSFSDTERSIIATLRELQISSPSSHNEIAMNGN
                     TKISFFIMPGKDKQGAIEDLIIEHASTRALYEYIIEFFEKIKNNKDDISASDKEYTYPT
                     NEKKAKVQVYLSCNRESDSRIGISMKNGIINTADNCFDEIKDFISKI"
                     /name="DUF3226 domain-containing protein"
     gene            complement(2405..3520)
                     /locus_tag="RRL08_RS28155"
                     /old_locus_tag="RRL08_28155"
     CDS             complement(2405..3520)
                     /locus_tag="RRL08_RS28155"
                     /old_locus_tag="RRL08_28155"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_019405083.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="ATP-binding protein"
                     /protein_id="WP_012579087.1"
                     /translation="MIKEISLKNFKCFNELYLKQLKTLNIIAGKNNYGKTSILDAIFCF
                     YDVKNPAVLLNIQAFRKEMAEINKNKPFWVSYFHDMDTSQKMSIVIRDERSEVTQTYET
                     ETNQRLESSLSLNVDTVLSNQNIPRQTIGSQATVNSLKINVTETPNAKNRVSNKLFSMQ
                     LKEDGVEIKSEIKNERDGINYKFKTATIITTSRKINKEATITNVSSLLTQKRKKDILEN
                     LKKIDDRIVDIAISAIGNNKEIYLDIGFSELNEISMLGEGISRALSFISSVLVQENSII
                     LIDEIENGIHYSVIKDIIKSLISSAKQNNNQIFATTHSQDVIRAINEIDSKNEDIAYIR
                     LGREKNSLKPTAVQFNMDDFSYSVENDWEVR"
                     /name="ATP-binding protein"
     gene            complement(3865..3978)
                     /locus_tag="RRL08_RS28160"
                     /old_locus_tag="RRL08_28160"
                     /pseudo=""
     CDS             complement(3865..3978)
                     /locus_tag="RRL08_RS28160"
                     /old_locus_tag="RRL08_28160"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_007772075.1"
                     /note="internal stop; Derived by automated computational
                     analysis using gene prediction method: Protein Homology."
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="replication initiation protein"
                     /name="replication initiation protein"
     Typing          complement(3866..4168)
                     /name="ColRNAI_rep_cluster_1987"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="96.382"
                     /coverage="99.0"
                     /evalue="2.88e-139"
ORIGIN
        1 gcgtcagatt ccgtgatgct cgtcaggggg gcggagccta tggaaaaacg gccgctgtgc
       61 ggcctttcct tctttcctcc atgcgattac tcggttttct cgagcgtttc tacgcatgct
      121 cctgccgctc gccgcagccg aacggcagga gcgtagcgac tgagtgagcg aggaagcgga
      181 aaagaggaga tccctacact gaccactgac gctctgaggc ctcttatgac gaaacaacag
      241 aaaacagcgc tgaacatggc taaattcatc cagaatcagt ctctgctcct gctggagaag
      301 cttaacgagc ttgatctcga tgtcgaggcc gacctttgtg agaaactcca cgatgatgcg
      361 gagcatcttt tccgtacact gtcctcgaga ctggatgcat tacaggatgg taactgatgg
      421 ccagagtgtc tattagtgag gctgcccgac tgacgggtaa gagtagaaca acactgcaca
      481 ggttaattaa agcaggtgac ctgtccacct gtagcggtga gcgcaatgca aaaatggtag
      541 atacttcaga gcttttacgt gtctttggcc cctttgagca accgaagggt gaacaccatt
      601 ctggacaggt ctctggacag cgtgatacag cctctgctga ccagagtgaa caggtgatcc
      661 gtcatctgaa acaggagatt gaacacctga acaccttact tttgtccaag gattcgcaca
      721 ttgacagcct gaaacaggcc atgctccttc ttgaaaatca ccaggcaaaa ttaactgaat
      781 ccccggcgcc atggtggaaa ttctggaaaa aatcctgacc ccgtcatgct tcagttttcc
      841 tctccggcca tcccggggag ttcctgaacc ttcccaaaaa tcgtcagatc tctgaacgct
      901 cctcaccact aaaaataccc acaccccacg caaaattaat attttgcaga tttgtattta
      961 atatcagtgg gttactttcc tgaaatttcg ttttttaaat tttatttata tagatccgac
     1021 tctatgacga ctcgtcatag agtccccggc gagtcgtcat agagtcggta acgactcagg
     1081 actataaaaa caataagtta ataacgaccc gactctagac acgactcccc gtttggttgt
     1141 tttttagacg cggcgactct gggtacgact ctagtgaaga gtcgccggtg aatcgtgtgg
     1201 tgagtcgtcc ggcgacttgc cataacgtga ttgccggccg tcgacgaacc cgattcctga
     1261 acgtgctgaa aaccggtttt ccggctgcgc cggcaacgct tcacggccac gcaataaatt
     1321 gcgtccccgt tcaccgtttt cggatggaaa gaacgccgga aacaggactt actctggctg
     1381 aatggcgtga attttcgcgc tatgcacttg cgtgcatact catgcatgcc gtaaaaacag
     1441 agcctgcgcg tttctggcgg gttttcgggt ggtttgttgc ctgttttacc ggttttccgt
     1501 cagaaacgcc ctgaggccgt tttagcggtg cgtacaatta tgattttatg ttaaattgtt
     1561 ttaagtgaat agagagaata taacttaagg gagcatcttg tgctgggtct tttacattag
     1621 atctgcacaa tcattgtttt ggcatctggt gatgtcttta ggacgtttga gattgctgat
     1681 aactaaagtg tatgatgctt tctatacgtt atccggcgtt taataacacc ctggtgataa
     1741 gccagcccgt gaagggctgg cttgatttgg atttatattt ttgaaataaa atcttttatt
     1801 tcatcaaagc aattgtctgc tgtgtttatt attccatttt tcatggatat tcctattctt
     1861 gagtcggatt ctctattgca gctaagatag acttgtacct tagctttttt ttcgtttgtt
     1921 ggataagtgt actctttgtc actcgctgag atgtcatctt tattattttt aattttttcg
     1981 aaaaattcta ttatgtattc atataacgct cgagtgcttg cgtgttcaat tatcagatct
     2041 tcaatggcac cttgcttgtc ttttcctggc attataaaga aagaaatttt tgtattgcca
     2101 ttcatagcta tctcgttatg cgagctgggg gaggagattt gtagttctcg caatgtggca
     2161 attattgatc tttctgtgtc agaaaatgat gtgtcagcat ctaatataat aaaaatactt
     2221 tctttttcat cgaaagaatc aatgtttttg aatgctctaa gtgcttgttt taattttgat
     2281 tttccattta ttttttcgac aaaaacatcg gtaatgcctt gtatttcaag taggttgcat
     2341 agaaaatgaa aatcatcatc accctcaacg aaaatgatct ttttgctatt atttatgtct
     2401 ttcattatct tacctcccag tcgttctcaa ctgagtagga gaaatcatcc atattgaatt
     2461 gtacggctgt tggttttagg gagttctttt ctcttcctag tctaatataa gcgatatctt
     2521 catttttgct atctatttcg tttattgctc gtatcacatc ttgactatga gttgttgcaa
     2581 atatttgatt gttgttttgt tttgcagatg aaattaatga ttttattatg tctttaatta
     2641 ctgagtaatg tattccgttc tcgatttcat caataagaat aattgagttt tcctgtacca
     2701 gcactgagct gataaaagat aatgctcgac tgataccctc gccaagcatt gatatttcat
     2761 ttagctcact aaatccaatg tctaaatata tttccttatt gttacctatc gcagatattg
     2821 ctatatctac aattctgtca tctatttttt ttaagttttc tagtatgtct tttttccttt
     2881 tttgtgttag taggctagat acatttgtaa ttgttgcctc tttgtttatc tttctggatg
     2941 ttgttattat tgttgctgtc ttaaatttat aattaatccc atccctttcg ttttttattt
     3001 cggattttat ttctacgcca tcttctttca attgcataga gaaaagctta ttggaaaccc
     3061 tgtttttcgc attgggtgtc tcggtcacat ttatttttaa agagtttact gtggcctgag
     3121 aaccgatagt ttgacgaggt atgttttggt tagatagtac ggtgtcaacg tttagagaca
     3181 aacttgattc taatctctga tttgtttctg tttcatatgt ttgtgttact tcagagcgtt
     3241 catctcgaat gactatggac atcttttgtg atgtgtccat atcatgaaag taactaaccc
     3301 aaaatggctt gtttttgttt atttctgcca tttcttttct gaatgcttga atgtttaaca
     3361 aaacagccgg gttttttaca tcataaaaac aaaaaatagc atccagtata gatgttttcc
     3421 cgtagttgtt tttcccagct atgatattta aagtctttaa ttgctttaga tatagctcat
     3481 tgaagcattt gaagttcttt aaacttattt cctttatcat gatagcctct gttcgtgttt
     3541 ttgttatatg ccatacgatt tgttagtacc ttaataaaat gtacagcttt cattgtgatt
     3601 agctagactt tatgtcaaag attaactttg attgcttgtg ttttaatcga ttttttttac
     3661 tttcttcttg agattatctg gcagcagccg taagcttccg gctgtgaacg aaaaaaaccg
     3721 ccttggcggg cggttttttc gaaaggttca gtagagttgg cgctctatga accgaggtaa
     3781 ctggcttaaa gggagcgcag tcaccaaaac tgttcgttta gtttagcttt aactggcgta
     3841 taacttcaag actaactccc taaatcagtt accagtggct gctgccagtg gcgctttgtc
     3901 gtgtctttcc gggttggact caagacgata gttaccggat taggcgcagc agtcggactg
     3961 aacggggggt tcgtgcatac agtccagctt ggagcgaact gcctacccgg aactgagtgt
     4021 caggcgtgga atgagacaaa cgcggccata acagcggaat gacaccggta aaccgaaagg
     4081 caggaacagg agagcgcacg agggagccat cagggggaaa cgcctggtat ctttatagtc
     4141 ctgtcgggtt tcgccaccac tgatttga
//
