LOCUS       NZ_CP135484             5216 bp    DNA     circular CON 07-OCT-2023
DEFINITION  Klebsiella pneumoniae strain isolateE plasmid pIsolateE_C, complete
            sequence.
ACCESSION   NZ_CP135484
VERSION     NZ_CP135484.1
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 5216)
  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  JOURNAL   Unpublished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 5216)
  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
            CP135484.1.
            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..5216
                     /organism="Klebsiella pneumoniae"
                     /mol_type="genomic DNA"
                     /strain="isolateE"
                     /host="Homo sapiens"
                     /db_xref="taxon:573"
                     /plasmid="pIsolateE_C"
                     /geo_loc_name="Canada: Ottawa"
                     /collection_date="2021"
     gene            complement(528..869)
                     /locus_tag="RRL12_RS26825"
                     /old_locus_tag="RRL12_26825"
     CDS             complement(528..869)
                     /locus_tag="RRL12_RS26825"
                     /old_locus_tag="RRL12_26825"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_006122514.1"
                     /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_071599364.1"
                     /translation="MADKRNKMLTMWVTEDEHRRLLERCDGKQLAAWMRQTCLDEKPTR
                     AGRLPSISPALLRQLAGMGNNLNQIARKVNAGGAGHDRVQIVAALMAIDAGLERLRHAV
                     LEKGPDDDC"
                     /name="MobC family plasmid mobilization relaxosome protein"
     gene            1492..1623
                     /locus_tag="RRL12_RS26830"
                     /old_locus_tag="RRL12_26830"
     CDS             1492..1623
                     /locus_tag="RRL12_RS26830"
                     /old_locus_tag="RRL12_26830"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_005761324.1"
                     /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_072007956.1"
                     /translation="MHEPPVQSDCCALSGNYRLESNPKRHAKAPLAAATGNRIHGAE"
                     /name="replication initiation protein"
     gene            complement(1843..2652)
                     /locus_tag="RRL12_RS26835"
                     /old_locus_tag="RRL12_26835"
     CDS             complement(1843..2652)
                     /locus_tag="RRL12_RS26835"
                     /old_locus_tag="RRL12_26835"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_010222407.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_032446875.1"
                     /translation="MSKDKKERSKNRYHQLVEKIFFDKYVDGDLEVLFERLDINSAAKD
                     LGIELPSNVGDVIYSIRFRTPMPESILLTQPEGKEWIIELAGRSKYRFRLVTISRILPN
                     PNMVAIKIPDNTPEIITGYSLDDEQALLAKVRYNRLIDIFLGITTYSLQNHLRTTVKGI
                     GQIEIDELYVGIDKYGCHYIIPVQAKGGTDQISMVQTSQDTAWCEQKYPNVRCRAISAQ
                     FVSSDLIALFELKIDEGQVKLIEERHYKLVPVKELDSSDISNYRMSV"
                     /name="hypothetical protein"
     gene            complement(2645..3895)
                     /locus_tag="RRL12_RS26840"
                     /old_locus_tag="RRL12_26840"
     CDS             complement(2645..3895)
                     /locus_tag="RRL12_RS26840"
                     /old_locus_tag="RRL12_26840"
                     /EC_number="2.1.1.37"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_015160339.1"
                     /GO_function="GO:0003886 - DNA
                     (cytosine-5-)-methyltransferase activity [Evidence IEA];
                     GO:0008168 - methyltransferase activity [Evidence IEA];
                     GO:1904047 - S-adenosyl-L-methionine binding [Evidence
                     IEA]"
                     /GO_process="GO:0006304 - DNA modification [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="DNA cytosine methyltransferase"
                     /protein_id="WP_001584442.1"
                     /translation="MTRPIAVDLFAGAGGLSLGFEQAGFDIMASVEIDPIHCSAHKYNF
                     PMCKTICRSVVDVTGEYVREVSGIGEKEIDVVIGGAPCQGFSLIGKRALDDDRNKLVYH
                     YVRLVLELKPKYFVFENVKGLTVGKHKQFLVEIMDAFKDGGYDVVSDYKVLNAADYGVP
                     QDRRRLFLMGGRKGIALPSYPEPLSIRTTVGDAIGDIPDAEKYPELWGRDWVYAKFGEQ
                     SLYSSYLHGVGKDPSDFSYPRIFNKDKLTCSLLTDHSDISRGRFVETLPDTVEPISRFK
                     KLSMNGLCNTLRAGTASDRGAFTSPRPIHPIYPRVITVREAARLHSYPDWFRFHVTKWH
                     GFRQVGNSVPPMLARSVGLQIMKVLGVTPKKPTKKIKLGDESLVAISMSDAASMFGVSS
                     NVIAKRIKNSNKEVVCE"
                     /name="DNA cytosine methyltransferase"
     gene            complement(4347..4562)
                     /locus_tag="RRL12_RS26845"
                     /old_locus_tag="RRL12_26845"
     CDS             complement(4347..4562)
                     /locus_tag="RRL12_RS26845"
                     /old_locus_tag="RRL12_26845"
                     /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="MbeD family mobilization/exclusion protein"
                     /protein_id="WP_015328239.1"
                     /translation="MTELEKQLLSALEQLQQDYSRRLDEWESAFEEWRKMSGLMQRENA
                     ALSERVSGLSRQVQSLSEQLRRLSTG"
                     /name="MbeD family mobilization/exclusion protein"
     gene            complement(4569..5066)
                     /locus_tag="RRL12_RS26850"
                     /old_locus_tag="RRL12_26850"
     CDS             complement(4569..5066)
                     /locus_tag="RRL12_RS26850"
                     /old_locus_tag="RRL12_26850"
                     /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="MbeB family mobilization protein"
                     /protein_id="WP_015328238.1"
                     /translation="MSSLLTASRDFEEKSKAQQQLTEERLKAAFSKHENVVKSELNASA
                     KRINDAISAHEQGMNAAMQSNRLSVLRMVGRTWLTITMVSGLLFASLSGVLWYQGNRIA
                     ANLAEIRQQRDTLSKLHMQTWGVTYLENRNGRFLVLPEGMKAETGRTVDNKTRNAVKLV
                     RE"
                     /name="MbeB family mobilization protein"
     Typing          complement(954..1129)
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="90.449"
                     /coverage="81.0"
                     /evalue="5.74e-59"
     Typing          1076..1601
                     /name="ColRNAI_rep_cluster_1987"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="89.434"
                     /coverage="99.0"
                     /evalue="0.0"
     Typing          complement(3..538)
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="99.0"
                     /evalue="3.18e-112"
     Typing          complement(535..848)
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="92.453"
                     /coverage="99.0"
                     /evalue="1.04e-58"
     Typing          complement(4232..5214)
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="99.0"
                     /evalue="0.0"
ORIGIN
        1 tcagcaaacc ccgtgtaatc gtctctgcgg cttcctgctt cgtttctggc agtcctgaag
       61 gcgtgaccag cgcccgccgg ttctccgggt cgttcggatc atgtagcccc agcctgccgt
      121 tgaccactgt ctgccacgca tcgatgcgcg gccggtcggc acgatcgtaa tacggctgga
      181 ggcgtttccc cgtcagtaat tcggtattgg ggatcagaaa attcagctca agacgaccct
      241 tgtctgcgtg ttccacccac agaatgctgt actggtcttt atcgagtccg ggcatcagaa
      301 cccgctcaaa gctggccatc agtttttcac gctgacccgg cggcaggtcc gcctccgcga
      361 atgacagcac cccggaggta tattttttca catacggcga cgcatcaatc agctcccgga
      421 cttcttccgg cttcccctgc aggacgctgg caccttcacg ctgccggtct ttacccagaa
      481 gataatccac aggaccggcg cccccgccgc gaccccgggg atggaattta acaatcatcg
      541 tccggccctt tttccagtac ggcatgccgc aaccgttcca gaccggcatc gatcgccatc
      601 agcgctgcca cgatctgcac ccggtcatga ccggcaccac cggcgttcac tttccgggcg
      661 atctggttca ggttattgcc catgccggca agctgacgca gcagcgcggg cgaaatcgag
      721 ggaagcctgc cggcgcgtgt cggtttctca tcaaggcagg tctggcgcat ccacgccgcc
      781 agttgttttc cgtcgcaccg ctcaagcaac cgccggtgtt cgtcttccgt cacccacatc
      841 gtgagcatct tgttgcgttt atctgccaga atcgcctcct gataacgccg tgacggacgg
      901 gaaagccttt cccggtcggc gcggggttgg acaagccgca ggcgcgtcag tggggtttcg
      961 gggcgcagcc ctgaaccagt cacgtagcgc tagcggagtg tatactggct tagtatgtta
     1021 cggcgagatg gagattcggg gaagtgcttc atgtggcaag ggggaaaata cggctgcggg
     1081 gcgtaagtgc aaaatgcagg taacgatgaa atgacgcctc ctcgctcact cggtcgctgc
     1141 gctcctgccg tgagactgcg gcgggcgtta ccagctcacg aaggacgaga taacgagatc
     1201 gcgctcaagt caggaaagtc aggaaagtca ggaaaaagga tgcggcgttg ccgtttttcc
     1261 ataggctccg cccccctgac aagcatcaca aaatctgacg ctcaaatcag tggtggcgaa
     1321 acccgacagg actataaaga tcccaggcgt ttccccctgg tagctccctc gtgcgctctc
     1381 ctgttcctgc ctttcggttt accggtgtca ttccgctgtt atggccgcgt ttgtctcatt
     1441 ccacgcctga cactcagttc cgggtaggca gttcgctcca agctggactg tatgcacgaa
     1501 ccccccgttc agtccgactg ctgcgccttg tccggtaact atcgtcttga gtccaacccg
     1561 aaaagacatg caaaagcgcc actggcagca gccactggta atcggattca cggagcggag
     1621 tagagttatc tacagagttc ttgaagtggt ggcctgacta cggctacact gaaaggacag
     1681 ttttggtatc tgcgctccgt gaaagccagt taccttcgga agaaagagtt ggtagctcta
     1741 aattccggca aacgaaccac cgttggtagc ggtggttttt ttgtttacgg cttaggagat
     1801 tacggctaga acgaaaggat ctcaagaaga tcctctcaga aattatacag acatgcggta
     1861 gtttgagatg tcagagctat ctaactcttt taccggaacc agtttgtaat gcctttcctc
     1921 aatcaatttc acttgtcctt cgtctatctt tagctcaaac agtgcaatca aatcgctcga
     1981 aacaaactga gcggaaatag ctctacatct aacatttggg tatttttgtt cacaccacgc
     2041 tgtatcttgc gatgtttgca ccattgatat ttgatctgtc ccaccttttg cttgaactgg
     2101 tattatataa tggcaaccgt atttatctat acctacataa agttcatcga tctctatttg
     2161 accaattccc ttcaccgtag ttcttaaatg attctgtaaa gaatatgtgg ttatacctag
     2221 aaatatatct attagccggt tatatctcac cttcgccagc aatgcctgct cgtcgtctaa
     2281 agaataacct gtaattatct ccggggtatt gtctggaatt tttattgcca ccatattagg
     2341 atttggcaaa atcctactaa tagttactaa tctaaatcga tactttgacc taccagccag
     2401 ctcaataatc cactccttac cttctggctg agtcaacaga atactttctg gcataggcgt
     2461 tctaaatctg attgaatata taacatcacc aacattagat gggagttcta tacctaaatc
     2521 ttttgcagca ctgtttatat ctaacctttc aaacaaaacc tctaagtcac catcaacata
     2581 tttatcgaaa aatatctttt ctaccaactg atggtatcta tttttggacc tttctttttt
     2641 atccttactc acaaacaacc tccttgttac tattttttat tctcttagca attacatttg
     2701 atgacacacc aaacatagat gcagcatcgg acatagaaat agcaaccaaa ctttcatcac
     2761 cgagtttgat tttcttcgtt ggtttttttg gcgtaacacc aagaaccttc ataatctgca
     2821 agccaacact tctagctagc ataggaggaa cactattacc gacctgtcta aatccatgcc
     2881 acttagtcac atgaaatctg aaccaatcag gatatgaatg cagtcttgct gcctctctga
     2941 ccgtgatgac cctaggatag atcggatgta taggacgagg agatgtaaaa gcacctctgt
     3001 cacttgctgt tcctgccctt aaagtattac atagcccatt catcgagagc tttttaaacc
     3061 tgctgattgg ttctaccgtg tcaggcaaag tttcaacaaa ccgccctcta gaaatgtcag
     3121 agtgatctgt cagtaaagaa cacgttaatt tgtctttatt aaaaatcctt gggtagctaa
     3181 aatcactagg atcttttcct acgccatgca aataggatga gtatagtgat tgctcaccaa
     3241 atttagcata aacccaatct ctaccccata gctcaggata tttttccgca tcaggaatat
     3301 ccccaatagc gtccccaacc gttgttctaa tggataatgg ctcagggtat gatggcagag
     3361 caattccttt ccttcccccc attaagaaaa gacgacggcg atcttgagga actccataat
     3421 cagctgcgtt tagcacttta taatcgctta caacgtcgta cccgccatct ttaaatgcat
     3481 ccattatctc tactaaaaac tgcttatgct taccaaccgt caaccctttt acattttcaa
     3541 aaacaaagta tttaggcttt agctcaagaa ccagccgtac atagtgatag accagtttgt
     3601 ttctatcatc atcaagcgcg cgttttccta ttaatgaaaa gccttggcag ggagcgcctc
     3661 cgatcactac atcaatctct ttctcaccaa tacctgaaac ttccctaacg tattctccgg
     3721 taacatcaac aacacttcta catatcgttt tgcacatagg aaagttatat ttgtgagcag
     3781 agcaatgtat tggatctatt tcaactgatg ccattatatc aaagccagct tgctcgaaac
     3841 cgagactcag cccacccgct ccagcaaata aatcaacagc aatcggtcta gtcattcttt
     3901 acacccacgt tatataaaat caacatgatg ctatcagaaa aacgatcgct ttaccgatcg
     3961 tttttctgat ttcgattgaa cataacatct cttacccgca ccgcgccgga ggcactcagg
     4021 gcgtttctga tggctgacgg gcaaaaggtg gtggcaagta caccgaaaac caccagaaac
     4081 gcacctgatt tattttacgc atatgcatca cttattcaca tcactgcata gccggtgatt
     4141 tcggttaaaa aagactctct gtgtgctgaa atcgcagaaa atggccatga tccccgtcac
     4201 gctcaggcca cctgagacgg gcgtttatca gtctccatac tccctgtcac catgagataa
     4261 tgtgcgttgc cgttccggta ccagatctgc tgtcttctct ggttcctttt ccgttgtttg
     4321 cccgtatcgc tgttgctcaa tctcattcag cctgtcgata accggcgcag ctgctcgctc
     4381 aaactctgca cctgcctgct caagcccgac acgcgctcgc tcagcgccgc gttctcccgt
     4441 tgcataagac cagacatctt ccgccattcc tcgaaggcgc tctcccactc gtccagcctt
     4501 ctcgagtagt cctgctgtag ctgctctaac gcgctcagca attgtttttc cagttccgtc
     4561 attctgctct actcccgtac cagcttcacc gcgttccgcg tcttgttgtc caccgtccgg
     4621 cccgtttcgg ctttcatccc ctccggcagc accagaaacc gtccgttgcg gttctccaga
     4681 taggtcacgc cccacgtctg catgtgcagt ttcgacagcg tatctctctg ctgcctgatt
     4741 tccgccaggt tcgccgctat ccggttcccc tggtaccaca gcaccccgct caggctggcg
     4801 aacagcagcc ctgacaccat ggtgatggtc agccacgtcc gcccgaccat tcgcagcacg
     4861 ctcagccggt tcgactgcat cgccgcgttc atcccctgtt cgtgggcgct gatggcgtcg
     4921 ttgattctct tcgcgcttgc gttcagttcc gatttgacaa cgttctcgtg cttgctgaat
     4981 gcggctttca gcctctcttc ggtaagctgc tgctgtgctt tcgatttctc ctcgaagtcc
     5041 ctcgaggccg ttaaaagact gctcataaat ggctcccctc agtcggatat ttcgcccccc
     5101 gtccgggtcg gcaatgctga tactgttttt tgtggttctg accacctcaa aaccggccgc
     5161 tgtgagcgcc cctgtgacgt catcacgcgt tttcagctct cctgatgagg ctaaca
//
