LOCUS       NZ_CP135485             4411 bp    DNA     circular CON 07-OCT-2023
DEFINITION  Klebsiella pneumoniae strain isolateE plasmid pIsolateE_D, complete
            sequence.
ACCESSION   NZ_CP135485
VERSION     NZ_CP135485.1
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 4411)
  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  JOURNAL   Unpublished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 4411)
  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
            CP135485.1.
            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..4411
                     /organism="Klebsiella pneumoniae"
                     /mol_type="genomic DNA"
                     /strain="isolateE"
                     /host="Homo sapiens"
                     /db_xref="taxon:573"
                     /plasmid="pIsolateE_D"
                     /geo_loc_name="Canada: Ottawa"
                     /collection_date="2021"
     gene            444..941
                     /locus_tag="RRL12_RS26855"
                     /old_locus_tag="RRL12_26855"
     CDS             444..941
                     /locus_tag="RRL12_RS26855"
                     /old_locus_tag="RRL12_26855"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_020325392.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MbeB family mobilization protein"
                     /protein_id="WP_020325392.1"
                     /translation="MSSLLTASRDFEEKSKAQQQLTEERLKAAFSKHENVVKSELNASA
                     KRINDAISAHEQGMNAAMQSNRLSVLRMVGRTWLTITMVSGLLFASLSGVLWYQGNRIA
                     ANLAEIRQQRDTLSKLQMQTWGVTYLENRNGRFLVLPEGMKAETGRTVDNKTRNAVKLV
                     RE"
                     /name="MbeB family mobilization protein"
     gene            948..1163
                     /locus_tag="RRL12_RS26860"
                     /old_locus_tag="RRL12_26860"
     CDS             948..1163
                     /locus_tag="RRL12_RS26860"
                     /old_locus_tag="RRL12_26860"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_015328239.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /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            1668..2039
                     /locus_tag="RRL12_RS26865"
                     /old_locus_tag="RRL12_26865"
     CDS             1668..2039
                     /locus_tag="RRL12_RS26865"
                     /old_locus_tag="RRL12_26865"
                     /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_021314598.1"
                     /translation="MSKKNDLNLSESTLESLREYVDDFGMTVDDVVLKLINENKSLKES
                     LGQDFVLSGEKEAHHFKDYVIHKLPKGKILVTHNGLKASNMKKILIEAGRELGMDENEL
                     NPDFTTYEIGRFLFKHLHA"
                     /name="hypothetical protein"
     gene            complement(2136..2561)
                     /locus_tag="RRL12_RS26870"
                     /old_locus_tag="RRL12_26870"
     CDS             complement(2136..2561)
                     /locus_tag="RRL12_RS26870"
                     /old_locus_tag="RRL12_26870"
                     /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_046181484.1"
                     /translation="MSFQQVLNEVKVISSNGDTSLAITRYDQQGLNRFLLRDLSHQTET
                     RSNYVNNLEQLCQQAKCNRVILNVNEISESFYMKLITFCNFTLLDAKQDMQHLNGFNYF
                     IVLNSFDENSGHTVWAPSYSPNCVTERDLDEYDPDRW"
                     /name="hypothetical protein"
     gene            complement(2574..2828)
                     /locus_tag="RRL12_RS26875"
                     /old_locus_tag="RRL12_26875"
     CDS             complement(2574..2828)
                     /locus_tag="RRL12_RS26875"
                     /old_locus_tag="RRL12_26875"
                     /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_101361146.1"
                     /translation="MNITINTPSVKTILDVQCDHCNFTGTIDYEAPRISKLTVGGKITF
                     DNALCPQCKTGEIFAPGGQYVRDDATGRMNRTGDANISL"
                     /name="hypothetical protein"
     gene            complement(3083..3216)
                     /locus_tag="RRL12_RS26880"
                     /old_locus_tag="RRL12_26880"
                     /pseudo=""
     CDS             complement(3083..3216)
                     /locus_tag="RRL12_RS26880"
                     /old_locus_tag="RRL12_26880"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001326446.1"
                     /note="frameshifted; 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"
     gene            3836..4177
                     /locus_tag="RRL12_RS26885"
                     /old_locus_tag="RRL12_26885"
     CDS             3836..4177
                     /locus_tag="RRL12_RS26885"
                     /old_locus_tag="RRL12_26885"
                     /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"
     Typing          3567..3742
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="82.32"
                     /coverage="100.0"
                     /evalue="5.910000000000001e-33"
     Typing          complement(3105..3621)
                     /name="ColRNAI_rep_cluster_1987"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="90.962"
                     /coverage="99.0"
                     /evalue="0.0"
     Typing          3..1279
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="99.531"
                     /coverage="99.0"
                     /evalue="0.0"
     Typing          3858..4171
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="92.453"
                     /coverage="99.0"
                     /evalue="1.33e-58"
     Typing          4168..4409
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="98.765"
                     /coverage="89.0"
                     /evalue="5.83e-44"
ORIGIN
        1 gcccggactc gataaagatc agtacagcat tctgtgggtg gaacacgcag acaagggtcg
       61 tcttgagctg aattttctga tccccaatac cgaattactg acggggaaac gcctccagcc
      121 gtattacgat cgtgccgacc ggccgcgcat cgatgcgtgg cagacagtgg tcaacggcag
      181 gctggggcta catgatccga acgacccgga gaaccggcgg gcgctggtca cgccgtcagg
      241 actgccagaa acgaagcagg aagccgcaga gacgattaca cggggtttgc tgatgttagc
      301 ctcatcagga gagctgaaaa cgcgtgatga cgtcacaggg gcgctcacag cggccggttt
      361 tgaggtggtc agaaccacaa aaaacagtat cagcattgcc gacccggacg gggggcgaaa
      421 tatccgactg aggggagcca tttatgagca gtcttttaac ggcctcgagg gacttcgagg
      481 agaaatcgaa agcacagcag cagcttaccg aagagaggct gaaagccgca ttcagcaagc
      541 acgagaacgt tgtcaaatcg gaactgaacg caagcgcgaa gagaatcaac gacgccatca
      601 gcgcccacga acaggggatg aacgcggcga tgcagtcgaa ccggctgagc gtgctgcgaa
      661 tggtcgggcg gacgtggctg accatcacca tggtgtcagg gctgctgttc gccagcctga
      721 gcggggtgct gtggtaccag gggaaccgga tagcggcgaa cctggcggaa atcaggcagc
      781 agagagatac gctgtcgaaa ctgcagatgc agacgtgggg cgtgacctat ctggagaacc
      841 gcaacggacg gtttctggtg ctgccggagg ggatgaaagc cgaaacgggc cggacggtgg
      901 acaacaagac gcggaacgcg gtgaagctgg tacgggagta gagcagaatg acggaactgg
      961 aaaaacaatt gctgagcgcg ttagagcagc tacagcagga ctactcgaga aggctggacg
     1021 agtgggagag cgccttcgag gaatggcgga agatgtctgg tcttatgcaa cgggagaacg
     1081 cggcgctgag cgagcgcgtg tcgggcttga gcaggcaggt gcagagtttg agcgagcagc
     1141 tgcgccggtt atcgacaggc tgaatgagat tgagcaacag cgatacgggc aaagaacgga
     1201 aaaggaacca gagaagacag cagatctggt accggaacgg caacgcacat tatctcatgg
     1261 tgacagggag tatggagact gataaacgcc cgtctcaggt ggcctgagcg tgacggggat
     1321 catggccatt ttctgcgatt tcagcacaca gagagtcttt tttaaccgaa atcaccggct
     1381 atgcagtgat gtgaataagt gatgcatatg cgtaaaataa atcaggtgcg tttctggtgg
     1441 ttttcggtgt acttgccacc accttttgcc cgtcagccat cagaaacgcc ctgagtgcct
     1501 ccggcgcggt gcgggtaaga gatgttatgg taaatccagc ggtgtagctg ttctttttga
     1561 accagcgatc agtgacttct atgttgcttg ttcaatacta aaaatatgtg tactatacta
     1621 cttgtgttgt ttttttcttt tctgacaact agcatagtgg tgactacatg agtaaaaaaa
     1681 acgatttaaa cctcagtgaa tcaacgttag aaagcctcag ggagtatgtc gatgacttcg
     1741 gcatgactgt tgatgatgtt gttctgaagt taattaatga gaataagtca ttgaaggaat
     1801 cacttggaca agactttgtg ttatctggcg aaaaggaagc gcaccacttt aaagattatg
     1861 tgattcataa actgcccaaa ggaaaaattc tggttaccca taatgggctt aaggccagca
     1921 acatgaagaa gatattgatt gaggcgggga gggagctagg catggatgaa aatgaactca
     1981 atccagattt cacaacctat gagatagggc gttttttgtt taagcaccta catgcgtaac
     2041 aatcctgcac gcctgaaggg caggaatcga acttagctgc ccggatgtta tggtaaattt
     2101 aggtgctata cggatttttt attaggcgat ctgagttacc aacgatctgg gtcgtattca
     2161 tctaaatcgc gctcagttac acaattgggg ctatacgatg gtgcccaaac tgtatgccca
     2221 ctgttttcat caaaagaatt aagaacaata aagtaattga agccattcaa atgttgcata
     2281 tcttgtttgg cgtctaacag agtgaaatta caaaaagtta ttaatttcat ataaaacgac
     2341 tctgaaattt cattcacgtt caaaataacc ctgttacatt ttgcctgctg gcataattgc
     2401 tcaagattat ttacatagtt actacgagtc tcggtctgat gagataagtc acgtaaaaga
     2461 aaacggttca atccttgttg gtcatatctg gtaatcgcta ggcttgtatc accattgctt
     2521 gaaataacct ttacctcatt caaaacttgc tgaaaactca tatgataagt tccttataga
     2581 ctaatgttcg catcgcctgt gcgattcatt cttccagtag catcatctct aacgtattga
     2641 ccacctggag cgaaaatttc acctgtttta cattgcgggc ataaagcatt gtcgaaggtt
     2701 atttttccgc cgacagtaag ctttgaaatt cgaggggctt cataatcaat agtgccagtg
     2761 aagttacagt gatcacactg tacatcaagg atggttttta ctgacggggt attgatagtt
     2821 atattcattc tcaacaatcc ttatcattac aagtggttgt gatgacttta tcagagaatg
     2881 cttagctaat gaaaacgaag gatcttcttg agatcgtgtt cctctcgtcg tagtcttcat
     2941 tcctgtaaac gaaaaaaccg ccttgctggg cggttttttc gaaggttctt ggagcagcaa
     3001 ctctttgaac cgaggtaact ggcttggagg agcgcagtca ccaaatctgt cctttcagtt
     3061 tagccttaac cggcgcataa cttcaagact caactcctct aaatccgtta cctgtggccg
     3121 ttgccattgg cgctttgtat gtctttccgg gttggactca agacgatagt taccggataa
     3181 ggcgcagcgg tcggactgaa cggggggttc gtgcatacag tccagcttgg agcgaactgc
     3241 ctacccggaa ctgagtgtca ggcgtggaat gagaaaaacg cggccataac agcggaatga
     3301 caccggtaaa ccgaaaggca ggaacaggag agcgcacgag ggagctacca gggggaaacg
     3361 cctgggatct ttatagtcct gtcgggtttc gccaccactg atttgagcat cagattctgt
     3421 gatgctcgtc aggggggcgg agcctatgga aaaacggcag cgccgcgtcc ttttctcttc
     3481 cttgccttca cggcatatgt ctctgcattt ctccgcgtgc cggttacgcc cgccgcagcc
     3541 gaacggcagg agcgtcagcg accgagtgag cgaggaggcg tcatatctcc tgcacaacca
     3601 ttatctgtct tacgcccggc agctgcatgt catacctgcc atatatagca ctttcgctga
     3661 tacccatacc aatgccaaca tagtaagcca gtatacactc cgctagcgct acgtgactgg
     3721 ttcagggctg cgccccgaaa cccgctaaaa gccactgacg cgcctgcggc ttgtccaacc
     3781 ccgcgccgac cgggaaaggc tttcccgtcc gtcacggcgt tatcaggagg cgattctggc
     3841 agataaacgc aacaagatgc tcacgatgtg ggtgacggaa gacgaacacc ggcggttgct
     3901 tgagcggtgc gacggaaaac aactggcggc gtggatgcgc cagacctgcc ttgatgagaa
     3961 accgacacgc gccggcaggc ttccctcgat ttcgcccgcg ctgctgcgtc agcttgctgg
     4021 catgggcaat aacctgaacc agatcgcccg gaaagtgaac gccggtggtg ccggtcatga
     4081 ccgggtgcag atcgtggcag cgctgatggc gatcgatgcc ggtctggaac ggttgcggca
     4141 tgccgtactg gaaaaagggc cggacgatga ttgttaaatt ccatccccgg ggtcgcggcg
     4201 ggggcgccgg tcctgtggat tatcttctgg gtaaagaccg gcagcgtgaa ggtgccagcg
     4261 tcctgcaggg gaagccggaa gaagtccggg agctgattga tgcgtcgccg tatgtgaaaa
     4321 aatatacctc gggggtgctg tcattcgcgg aggcggacct gccgccgggt cagcgtgaaa
     4381 aactgatggc cagctttgag cgggttctga t
//
