LOCUS       NZ_CP135487             3559 bp    DNA     circular CON 07-OCT-2023
DEFINITION  Klebsiella pneumoniae strain isolateE plasmid pIsolateE_F, complete
            sequence.
ACCESSION   NZ_CP135487
VERSION     NZ_CP135487.1
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 3559)
  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  JOURNAL   Unpublished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 3559)
  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
            CP135487.1.
            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..3559
                     /organism="Klebsiella pneumoniae"
                     /mol_type="genomic DNA"
                     /strain="isolateE"
                     /host="Homo sapiens"
                     /db_xref="taxon:573"
                     /plasmid="pIsolateE_F"
                     /geo_loc_name="Canada: Ottawa"
                     /collection_date="2021"
     gene            1..114
                     /locus_tag="RRL12_RS26920"
                     /old_locus_tag="RRL12_26920"
     CDS             1..114
                     /locus_tag="RRL12_RS26920"
                     /old_locus_tag="RRL12_26920"
                     /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_071653267.1"
                     /translation="MHEPPVQSDCCAFSGNYQLESNPERHDEAPLAAATGN"
                     /name="replication initiation protein"
     gene            complement(321..797)
                     /locus_tag="RRL12_RS26925"
                     /old_locus_tag="RRL12_26925"
     CDS             complement(321..797)
                     /locus_tag="RRL12_RS26925"
                     /old_locus_tag="RRL12_26925"
                     /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_077861907.1"
                     /translation="MTVLSTLNNLKSIPCINAFTGRANNSYLWRYVMEDHKDEFGATTI
                     KCFYLREEISEDYVSIYHSNKDYYEGMVRDVHKRIPVGKTKPAIYLSFDAAEVIEQVNK
                     PDKCIDIKDEGYPHLGLWYLFDINDEFTLIEVTTTILELSSFFQRNEGGVVVPL"
                     /name="hypothetical protein"
     gene            complement(797..1441)
                     /locus_tag="RRL12_RS26930"
                     /old_locus_tag="RRL12_26930"
     CDS             complement(797..1441)
                     /locus_tag="RRL12_RS26930"
                     /old_locus_tag="RRL12_26930"
                     /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_044816498.1"
                     /translation="MKYINHCDSEDYYITNDSIDLGVRYDVSDYNKLELNDLRDPDLFK
                     VLGRAFVVVENSVWESWNDDVKTLDCSGDGYESILKHYESLELSGEFLLFFKKIRSAIS
                     VYNREYEFCTGDLEPSLQAIVQLIRYAPELAAKKDAQIYFDKKSECFGLIYKQTKKSKG
                     TLNLIVKTNNEIIFSFVRKVSGVVKVTGRAYIGDSLDNSIAIKSLFKMMEW"
                     /name="hypothetical protein"
     gene            complement(1443..1667)
                     /locus_tag="RRL12_RS26935"
                     /old_locus_tag="RRL12_26935"
     CDS             complement(1443..1667)
                     /locus_tag="RRL12_RS26935"
                     /old_locus_tag="RRL12_26935"
                     /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_071653266.1"
                     /translation="MSNKDSLERKVTPRKNEPVFPMALRVGIAEDICFLELVDFPEKES
                     GRVFYSIALTKKHAKNLIDGLNKFVESGD"
                     /name="hypothetical protein"
     gene            complement(2531..2953)
                     /locus_tag="RRL12_RS26940"
                     /old_locus_tag="RRL12_26940"
     CDS             complement(2531..2953)
                     /locus_tag="RRL12_RS26940"
                     /old_locus_tag="RRL12_26940"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:YP_005229777.1"
                     /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_044816494.1"
                     /translation="MARVSISEAARLVKVSRPTIYKMINSGKLSYTSVVKHGKNTKVVD
                     TSELIRVFGSLYGGGDTVKHDVKGDAGATGVNISGLHDLQHKIALLEAENDGLKGAVKA
                     RDEHIDSLRQAMQLLEHKLEPSPQVHSPWWKFWKKS"
                     /name="helix-turn-helix domain-containing protein"
     gene            complement(2953..3144)
                     /locus_tag="RRL12_RS26945"
                     /old_locus_tag="RRL12_26945"
     CDS             complement(2953..3144)
                     /locus_tag="RRL12_RS26945"
                     /old_locus_tag="RRL12_26945"
                     /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_044816495.1"
                     /translation="MTKQQKTALNMAKFIQNQSLLLLEKLNELDLDVEADLCEKLHDDA
                     EHLFRTLSSGLDELQDGN"
                     /name="Rop family plasmid primer RNA-binding protein"
     Typing          2..114
                     /name="ColRNAI_rep_cluster_1987"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="92.105"
                     /coverage="100.0"
                     /evalue="2.98e-37"
     Typing          3266..3559
                     /name="ColRNAI_rep_cluster_1987"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="95.27"
                     /coverage="99.0"
                     /evalue="2.92e-129"
ORIGIN
        1 atgcacgaac cccccgttca gtccgactgc tgcgcctttt ccggtaacta tcaacttgag
       61 tccaacccgg aaagacacga cgaagcgcca ctggcagcag ccactggtaa ctgatttaga
      121 ggagttagtc ttgaagttat gtgccagtta aggctaaact gaaagaacga ttttggttac
      181 tgcgctcctc taactagcca gttaccttgg ttcatagagc cgcaaactct tagaacctaa
      241 gaaaaaccgc cccgcaaagg cggtttttct ttttcaagaa gagtactagg tcacacttga
      301 tgacgtcaag acggttttcg ctaaagagga acaaccacgc caccttcatt tctttgaaaa
      361 aaagaggata attccaaaat agttgtagtc acctcaatca aagtaaattc atcattaata
      421 tcaaataaat accacaaacc caagtgaggg taaccttcgt cctttatatc aatacattta
      481 tctggtttgt taacttgctc gatcacttcc gctgcatcaa atgagagata tatggcaggt
      541 ttggttttcc ctacagggat tcttttatgt acatccctta ccattccttc ataataatct
      601 ttatttgaat gataaataga cacataatcc tctgaaattt cctccctaag ataaaaacac
      661 ttaatagttg tagcgccaaa ctcatcttta tgatcttcca taacataacg ccataaatat
      721 gaattatttg ctctgcccgt aaatgcatta atacaaggga ttgatttgag gttatttaaa
      781 gttgataaca cagtcatcac cactccatca ttttaaataa tgatttgata gcaatggagt
      841 tatcaaggct atcgccaata tatgccctac ctgtaacctt aaccactcca gaaacttttc
      901 taacaaagga aaaaataatc tcgttatttg ttttcactat taaatttagc gtgcctttgc
      961 ttttcttagt ttgtttatat ataagcccaa aacactctga ttttttatca aagtaaatct
     1021 gagcgtcttt ttttgcagca agttcagggg catacctaat caactgaaca atagcctgca
     1081 aagatggttc taggtcacca gtgcagaact cgtattctct attataaaca gaaatggcac
     1141 ttcttatttt tttaaaaaac aataagaatt cacctgataa ttctaatgat tcgtaatgtt
     1201 ttaaaattga ctcataaccg tcaccagagc aatctaatgt tttaacatca tcattccaag
     1261 actcccaaac agaattctca acaacaacaa atgctcgacc caaaacttta aacaaatccg
     1321 gatctcttaa atcatttagc tctaacttat tataatcaga aacatcataa cgaacaccga
     1381 gatcaatgct atcattagta atataataat cttcactatc gcagtggtta atgtatttca
     1441 tactaatcac ctgactcaac gaatttattc aatccatcga taaggttctt tgcatgtttt
     1501 ttggttagag ctatggaata aaaaaccctt cctgattctt tttcaggaaa gtccactaac
     1561 tctaaaaaac aaatatcttc agctatccca actcttagag ccatcgggaa tacaggttca
     1621 ttttttcttg gtgttacttt tctttctaaa gaatctttat tgctcattat aataccccga
     1681 tagaaataaa tttaagttta gaacataaaa aataatacca taaaacaaca tctttcatcc
     1741 acaatgctca tttaacatta cattggtcac tttatggaat tttgtggcca tgatttaaca
     1801 taacaccaaa attgtacgca ccgctaaaac ggcctcaggg cgtttctgac gggaaaccgg
     1861 taaaataggc aacaaaccac ccgaaaaccc gccagaaacg cgcaggctct gtttttacgg
     1921 catgcatgag tatgcacgca agtgcatagc gcgaaaattc acgctattca gccagggtaa
     1981 gtcctgtttc cggcgttctt cccatccgaa aacggtgaac ggggacgcaa tttattgcgt
     2041 ggccgtgaag cgttgccggc gcagccggaa aaccggtttt cagcacgttc aggaatcggg
     2101 ttcgtcgacg gccggcaatc acgttatggc aagtcgccgg acgactcacc acacgattca
     2161 ccggcgactc ttcactagag tcgtacccag agtcgtcacg tctaaaaaac aaccaaacgg
     2221 ggagtcgggt ctagagtcgg gtcgttgtta acttattgtt tttatagtcc tgagtcgtta
     2281 ccgactctat gacgactcgc cggggactct atgacgagtc gtcatagagt cggatctgta
     2341 taaataaaat taaaaaaacg aaatttatag aacgtaaact actgatataa aatacaaatc
     2401 tgcaaaattt taattttgcg tggggtgtgg atatttttag tggtgaggag cgttcagcga
     2461 tctggcgatt tttgggaagg ttcaggaact ccccggaatg gccggagagg aaaactgaag
     2521 catgacgggg tcaggatttc ttccagaatt tccaccacgg agaatgaacc tgtggagagg
     2581 gttcgagctt gtgttccaga agctgcatag cctggcgaag agaatcgata tgttcatcac
     2641 gagctttaac agccccttta agaccatcgt tttcagcttc aagcaaagca attttatgct
     2701 gtaaatcatg taaaccagag atgttaaccc ctgtagcgcc tgcgtcacct tttacatcat
     2761 gttttacagt gtcgccccca ccataaagcg agccaaaaac cctaataagc tctgatgtat
     2821 caacaacttt agtatttttc ccatgcttta caacagaggt gtaacttagt ttcccactgt
     2881 taatcatctt gtaaattgtg gggcgactaa ccttaacaag ccgagccgct tcactaatag
     2941 acactctggc catcagtttc catcctgtaa ttcatccagt cccgaagaca gtgtacggaa
     3001 aagatgctcc gcatcatcgt ggagtttctc acaaaggtcg gcctctacat caagatcaag
     3061 ctcgttaagc ttctccagca ggagcagaga ctgattctgg atgaatttag ccatgttcag
     3121 cgctgttttc tgttgtttcg tcataagagg cctcagagcg tcagtgctca gtgtagggat
     3181 gttctctttt ccgcttcctc gctcactcag tcgctacgct cctgccgttc ggctgcggcg
     3241 agcggcagga gcatgcgtat aaaagctcga gaaaaccgag cgatcgcgtg atggggagaa
     3301 ggagaggccg cacagcggcc gtttttccat aggctccgcc cccctgacaa gcatcacgaa
     3361 atctgacgct caaatcagtg gtggcgaaac ccgacaggac tataaagata ccaggcgttt
     3421 ccccctggtg gctccctcgt gcgctctcct gttcctgcct ttcggtttac cggtgtcatt
     3481 ccgctgttat ggccgcgttt atctcattcc acgcctgaca ctcagttccg ggtaggcagt
     3541 tcgctccaag ctggactgt
//
