LOCUS       NZ_CP135486             4167 bp    DNA     circular CON 07-OCT-2023
DEFINITION  Klebsiella pneumoniae strain isolateE plasmid pIsolateE_E, complete
            sequence.
ACCESSION   NZ_CP135486
VERSION     NZ_CP135486.1
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 4167)
  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  JOURNAL   Unpublished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 4167)
  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
            CP135486.1.
            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..4167
                     /organism="Klebsiella pneumoniae"
                     /mol_type="genomic DNA"
                     /strain="isolateE"
                     /host="Homo sapiens"
                     /db_xref="taxon:573"
                     /plasmid="pIsolateE_E"
                     /geo_loc_name="Canada: Ottawa"
                     /collection_date="2021"
     gene            1..114
                     /locus_tag="RRL12_RS26890"
                     /old_locus_tag="RRL12_26890"
                     /pseudo=""
     CDS             1..114
                     /locus_tag="RRL12_RS26890"
                     /old_locus_tag="RRL12_26890"
                     /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"
     gene            459..1574
                     /locus_tag="RRL12_RS26895"
                     /old_locus_tag="RRL12_26895"
     CDS             459..1574
                     /locus_tag="RRL12_RS26895"
                     /old_locus_tag="RRL12_26895"
                     /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            1574..2206
                     /locus_tag="RRL12_RS26900"
                     /old_locus_tag="RRL12_26900"
     CDS             1574..2206
                     /locus_tag="RRL12_RS26900"
                     /old_locus_tag="RRL12_26900"
                     /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            2572..2814
                     /locus_tag="RRL12_RS26905"
                     /old_locus_tag="RRL12_26905"
     CDS             2572..2814
                     /locus_tag="RRL12_RS26905"
                     /old_locus_tag="RRL12_26905"
                     /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_098963735.1"
                     /translation="MHSAEIHTIQPGEVLFPAFFSSENGERGRNLLRGREALPAQPENR
                     FSAPSGIGFVDGRQSRYGKSPDDSPHDSPAIRIVN"
                     /name="hypothetical protein"
     gene            complement(3160..3561)
                     /locus_tag="RRL12_RS26910"
                     /old_locus_tag="RRL12_26910"
     CDS             complement(3160..3561)
                     /locus_tag="RRL12_RS26910"
                     /old_locus_tag="RRL12_26910"
                     /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(3561..3752)
                     /locus_tag="RRL12_RS26915"
                     /old_locus_tag="RRL12_26915"
     CDS             complement(3561..3752)
                     /locus_tag="RRL12_RS26915"
                     /old_locus_tag="RRL12_26915"
                     /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"
     Typing          2..114
                     /name="ColRNAI_rep_cluster_1987"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="94.737"
                     /coverage="100.0"
                     /evalue="2.9599999999999995e-42"
     Typing          3875..4167
                     /name="ColRNAI_rep_cluster_1987"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="92.857"
                     /coverage="99.0"
                     /evalue="4.9500000000000006e-117"
ORIGIN
        1 atgcacgaac cccccgttca gtccgactgc tgcgcctaat ccggtaacta tcgtcttgag
       61 tccaacccgg aaagacacga caaagcgcca ctggcagcag ccactggtaa ctgatttagg
      121 gagttagtct tgaagttata cgccagttaa agctaaacta aacgaacagt tttggtgact
      181 gcgctccctt taagccagtt acctcggttc atagagcgcc aactctactg aacctttcga
      241 aaaaaccgcc cgccaaggcg gtttttttcg ttcacagccg gaagcttacg gctgctgcca
      301 gataatctca agaagaaagt aaaaaaaatc gattaaaaca caagcaatca aagttaatct
      361 ttgacataaa gtctagctaa tcacaatgaa agctgtacat tttattaagg tactaacaaa
      421 tcgtatggca tataacaaaa acacgaacag aggctatcat gataaaggaa ataagtttaa
      481 agaacttcaa atgcttcaat gagctatatc taaagcaatt aaagacttta aatatcatag
      541 ctgggaaaaa caactacggg aaaacatcta tactggatgc tattttttgt ttttatgatg
      601 taaaaaaccc ggctgttttg ttaaacattc aagcattcag aaaagaaatg gcagaaataa
      661 acaaaaacaa gccattttgg gttagttact ttcatgatat ggacacatca caaaagatgt
      721 ccatagtcat tcgagatgaa cgctctgaag taacacaaac atatgaaaca gaaacaaatc
      781 agagattaga atcaagtttg tctctaaacg ttgacaccgt actatctaac caaaacatac
      841 ctcgtcaaac tatcggttct caggccacag taaactcttt aaaaataaat gtgaccgaga
      901 cacccaatgc gaaaaacagg gtttccaata agcttttctc tatgcaattg aaagaagatg
      961 gcgtagaaat aaaatccgaa ataaaaaacg aaagggatgg gattaattat aaatttaaga
     1021 cagcaacaat aataacaaca tccagaaaga taaacaaaga ggcaacaatt acaaatgtat
     1081 ctagcctact aacacaaaaa aggaaaaaag acatactaga aaacttaaaa aaaatagatg
     1141 acagaattgt agatatagca atatctgcga taggtaacaa taaggaaata tatttagaca
     1201 ttggatttag tgagctaaat gaaatatcaa tgcttggcga gggtatcagt cgagcattat
     1261 cttttatcag ctcagtgctg gtacaggaaa actcaattat tcttattgat gaaatcgaga
     1321 acggaataca ttactcagta attaaagaca taataaaatc attaatttca tctgcaaaac
     1381 aaaacaacaa tcaaatattt gcaacaactc atagtcaaga tgtgatacga gcaataaacg
     1441 aaatagatag caaaaatgaa gatatcgctt atattagact aggaagagaa aagaactccc
     1501 taaaaccaac agccgtacaa ttcaatatgg atgatttctc ctactcagtt gagaacgact
     1561 gggaggtaag ataatgaaag acataaataa tagcaaaaag atcattttcg ttgagggtga
     1621 tgatgatttt cattttctat gcaacctact tgaaatacaa ggcattaccg atgtttttgt
     1681 cgaaaaaata aatggaaaat caaaattaaa acaagcactt agagcattca aaaacattga
     1741 ttctttcgat gaaaaagaaa gtatttttat tatattagat gctgacacat cattttctga
     1801 cacagaaaga tcaataattg ccacattgcg agaactacaa atctcctccc ccagctcgca
     1861 taacgagata gctatgaatg gcaatacaaa aatttctttc tttataatgc caggaaaaga
     1921 caagcaaggt gccattgaag atctgataat tgaacacgca agcactcgag cgttatatga
     1981 atacataata gaatttttcg aaaaaattaa aaataataaa gatgacatct cagcgagtga
     2041 caaagagtac acttatccaa caaacgaaaa aaaagctaag gtacaagtct atcttagctg
     2101 caatagagaa tccgactcaa gaataggaat atccatgaaa aatggaataa taaacacagc
     2161 agacaattgc tttgatgaaa taaaagattt tatttcaaaa atataaatcc aaatcaagcc
     2221 agcccttcac gggctggctt atcaccaggg tgttattaaa cgccggataa cgtatagaaa
     2281 gcatcataca ctttagttat cagcaatctc aaacgtccta aagacatcac cagatgccaa
     2341 aacaatgatt gtgcagatct aatgtaaaag acccagcaca agatgctccc ttaagttata
     2401 ttctctctat tcacttaaaa caatttaaca taaaatcata attgtacgca ccgctaaaac
     2461 ggactcagga cgtttctgac gggaaaccgg taaaacaggc aacaaaccac ccgaaaaccc
     2521 gccagaaacg cgcaggctct gtttttacgg catgcatgag tatgcgcgca agtgcatagc
     2581 gcggaaattc acaccattca gccaggggaa gtcctgtttc cggcgttctt ctcctccgaa
     2641 aacggtgaac ggggacgcaa tttattgcgt ggccgtgaag cgttgccggc gcagccggaa
     2701 aaccggtttt cagcaccttc aggaatcggg ttcgtcgacg gccggcaatc acgttatggc
     2761 aagtcgccgg acgactcacc acacgattca ccggcgattc gaatcgtgaa ttgaatcaag
     2821 agtcaccatg agcaaaaaac acccaaagtg atgaattgaa tcaagagtcg attcatcata
     2881 acaatatgat aataaagcgt gattcacata tgaatcgtgg gcaattcgtc agcgattcgc
     2941 catagagtcg tccacgactt ggatctgcac tttgtaacac atcaccgcac atttattttt
     3001 cattaaccca ttgttgtaaa taaggaatct gcaaaatttt aattttgcgt ggggtgtggg
     3061 tatttttagt ggtgaggagc gttcagagat ctgacgattt ttgggaaggt tcaggaactc
     3121 cctgggatgg ccggagagga aaactgaagc atgacggggt caggattttt tccagaattt
     3181 ccaccatggc gccggggatt cagttaattt tgcctggtga ttttcaagaa ggagcatggc
     3241 ctgtttcagg ctgtcaatgt gcgaatcctt ggacaaaagt aaggtgttca ggtgttcaat
     3301 ctcctgtttc agatgacgga tcacctgttc actctggtca gcagaggctg tatcacgctg
     3361 tccagagacc tgtccagaat ggtgttcacc cttcggttgc tcaaaggggc caaagacacg
     3421 taaaagctct gaagtatcta ccatttttgc attgcgctca ccgctacagg tggacaggtc
     3481 acctgcttta attaacctgt gcagtgttgt tctactctta cccgtcagtc gggcagcctc
     3541 actaatagac actctggcca tcagttacca tcctgtaatg catccagtct cgaggacagt
     3601 gtacggaaaa gatgctccgc atcatcgtgg agtttctcac aaaggtcggc ctcgacatcg
     3661 agatcaagct cgttaagctt ctccagcagg agcagagact gattctggat gaatttagcc
     3721 atgttcagcg ctgttttctg ttgtttcgtc ataagaggcc tcagagcgtc agtggtcagt
     3781 gtagggatct cctcttttcc gcttcctcgc tcactcagtc gctacgctcc tgccgttcgg
     3841 ctgcggcgag cggcaggagc atgcgtagaa acactcgaga aaaccgagta atcgcatgga
     3901 ggaaagaagg aaaggccgca cagcggccgt ttttccatag gctccgcccc cctgacgagc
     3961 atcacggaat ctgacgctca aatcagtggt ggcgaaaccc gacaggacta taaagatacc
     4021 aggcgtttcc ccctgatggc tccctcgtgc gctctcctgt tcctgccttt cggtttaccg
     4081 gtgtcattcc gctgttatgg ccgcgtttgt ctcattccac gcctgacact cagttccggg
     4141 taggcagttc gctccaagct ggactgt
//
