LOCUS       NZ_CP086466             3991 bp    DNA     circular CON 28-MAY-2024
DEFINITION  Klebsiella pneumoniae strain MCL-2017-2-T5-MAC plasmid
            pMCL-2017-T5-MAC_2, complete sequence.
ACCESSION   NZ_CP086466
VERSION     NZ_CP086466.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN22108727
            Assembly: GCF_022759625.1
KEYWORDS    RefSeq.
SOURCE      Klebsiella pneumoniae
  ORGANISM  Klebsiella pneumoniae
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Klebsiella/Raoultella group; Klebsiella.
REFERENCE   1  (bases 1 to 3991)
  AUTHORS   Moser,A.I., Endimiani,A., Campos-Madueno,E.I. and Vallone,A.
  TITLE     Genome plasticity in E. coli and K. pneumoniae: SNV accumulation
            over time
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 3991)
  AUTHORS   Moser,A.I., Endimiani,A., Campos-Madueno,E.I. and Vallone,A.
  TITLE     Direct Submission
  JOURNAL   Submitted (04-NOV-2021) Institute for Infectious Diseases,
            University of Bern, Friedbuehlstrasse 51, Bern 3001, Switzerland
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: Unicycler v. 0.4.8
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 462x
            Sequencing Technology :: Illumina NovaSeq; Oxford Nanopore MiniION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_022759625.1-RS_2024_05_28
            Annotation Date                   :: 05/28/2024 04:40:20
            Annotation Pipeline :: NCBI Prokaryotic Genome Annotation Pipeline
            (PGAP)
            Annotation Method :: Best-placed reference protein set; GeneMarkS-2+
            Annotation Software revision      :: 6.7
            Features Annotated                :: Gene; CDS; rRNA; tRNA; ncRNA
            Genes (total)                     :: 5,601
            CDSs (total)                      :: 5,476
            Genes (coding)                    :: 5,350
            CDSs (with protein)               :: 5,350
            Genes (RNA)                       :: 125
            rRNAs                             :: 9, 8, 8 (5S, 16S, 23S)
            complete rRNAs                    :: 9, 8, 8 (5S, 16S, 23S)
            tRNAs                             :: 87
            ncRNAs                            :: 13
            Pseudo Genes (total)              :: 126
            CDSs (without protein)            :: 126
            Pseudo Genes (ambiguous residues) :: 0 of 126
            Pseudo Genes (frameshifted)       :: 61 of 126
            Pseudo Genes (incomplete)         :: 68 of 126
            Pseudo Genes (internal stop)      :: 19 of 126
            Pseudo Genes (multiple problems)  :: 18 of 126
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP086466.1.
            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..3991
                     /organism="Klebsiella pneumoniae"
                     /mol_type="genomic DNA"
                     /strain="MCL-2017-2-T5-MAC"
                     /host="Homo sapiens"
                     /db_xref="taxon:573"
                     /plasmid="pMCL-2017-T5-MAC_2"
                     /geo_loc_name="Switzerland"
                     /collection_date="2017"
                     /collected_by="Institute for Infectious Diseases Bern"
     gene            135..407
                     /locus_tag="LNN59_RS27905"
                     /old_locus_tag="LNN59_27905"
     CDS             135..407
                     /locus_tag="LNN59_RS27905"
                     /old_locus_tag="LNN59_27905"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_004897311.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_019405140.1"
                     /translation="MATDAQVKEINALIKKYPDSCSICHEVYDEDDVTYTVFGYDRKGK
                     IQVTTGCCAGMLTEPVLLGVCGCFDPEERDEIMQNHPMAKQFFTE"
                     /name="hypothetical protein"
     gene            988..1962
                     /locus_tag="LNN59_RS27910"
                     /old_locus_tag="LNN59_27910"
     CDS             988..1962
                     /locus_tag="LNN59_RS27910"
                     /old_locus_tag="LNN59_27910"
                     /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_114269875.1"
                     /translation="MAFFNLLFVASLICFGGVMGSYSRGCRDSQNKFSKDKDENNKRAS
                     VYRFGIASAFICVPFISSFLHVDYSSIIFPVADGGGTKFIEQILLLISVSGISAYLGYA
                     LLDGLANKVLKEQVDGIDKKQQDLEAEQDEFKDELDRSKELIEQLEMDKKTTKFELGYF
                     KAISAVDKAESMMSIPDEALSVKKKLTEALDAVTESLSLVKREDVAKDDYDKLLVLKAY
                     ILKRLDRIDDALSITDELLMSNEDNPILIYNKACYQYILRRCQADNSDIKDMIRRALTI
                     KVTDPEFIRRQEKIRTKVIGNKDNDLEGLFTDAELEELKVAIK"
                     /name="hypothetical protein"
     gene            complement(2189..2301)
                     /locus_tag="LNN59_RS27915"
                     /old_locus_tag="LNN59_27915"
                     /pseudo=""
     CDS             complement(2189..2301)
                     /locus_tag="LNN59_RS27915"
                     /old_locus_tag="LNN59_27915"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_005761324.1"
                     /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            2709..2900
                     /locus_tag="LNN59_RS27920"
                     /old_locus_tag="LNN59_27920"
     CDS             2709..2900
                     /locus_tag="LNN59_RS27920"
                     /old_locus_tag="LNN59_27920"
                     /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_040198051.1"
                     /translation="MTKQQKTALNMAKFIQNQSLLLLDKLNELDLDVEADLCEKLHDDA
                     EHLFRTLSSRLDELQDGN"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            2900..3322
                     /locus_tag="LNN59_RS27925"
                     /old_locus_tag="LNN59_27925"
     CDS             2900..3322
                     /locus_tag="LNN59_RS27925"
                     /old_locus_tag="LNN59_27925"
                     /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_040214596.1"
                     /translation="MAIVSISEAARLVKVSRPTIYKMINSGKLSYTSVVKHGKAIKVID
                     TSELIRVFGSLDGVIDTVKYDVKSDAESTGINSVGLHDLQHRIALLEAENDGLKGAVKA
                     RDEHIDSLRQAMQLLEHKHEPSSPPHSPWWKFWKKS"
                     /name="helix-turn-helix domain-containing protein"
     Typing          complement(2190..2661)
                     /name="ColRNAI_rep_cluster_1987"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="86.777"
                     /coverage="92.0"
                     /evalue="7.8799999999999974e-146"
ORIGIN
        1 gggttacgcc ccagaatcgt tctgaggccg ttttagcggt gcgtgtaatg ggacgttatg
       61 gtaaatcaac ggcggatgcc tgagtctgtg ttagagtcag cggattgtga taatcagtga
      121 ctcagggaga tgttttggct actgacgctc aggtaaaaga aattaatgca ctcatcaaaa
      181 aatacccgga ctcatgctcc atctgtcatg aagtctatga tgaggatgat gtgacctaca
      241 ccgtttttgg gtatgaccgg aaaggtaaaa tacaggtcac cacgggatgc tgtgccggaa
      301 tgctgacaga gccggttctg ctgggtgtct gtgggtgctt tgacccggaa gaacgtgacg
      361 agatcatgca gaatcacccc atggcaaagc agtttttcac agagtgattc cgtatctgtt
      421 gagtctgaag cccgccttgt gcgggctttt tcatatctgc gtgaaatgag gcgttatggt
      481 aaatgcacgc attcattctt ttgaaaaatc cagaatgacg aatacatggg gcatgtttat
      541 atgactattg agaggaagga tgttattgta aaaaaatcct ttaaattcaa tcatttaatt
      601 atggtagcca aaggtatggg gcttcgctta ttcctaagga ataagcgaag ccccgcccct
      661 ttggctacca gtgcattata cttttttttt cacccaatgt caatacatgg gttgatttta
      721 tcattttaag catttttgtt gttgtgagtg ctgggtttat gccctatatt cagcgctaag
      781 caagcatggg cttgcaaagg aacaattaat gagaggtgct ctatgaaaaa aatcaaactt
      841 cacgatgagc gtccagactt gtaagtgtca agtcagcaga aaaaggcagc caaggctgcc
      901 ttttttgtta ttggttagta tatgattgag cttatcttaa cttacctgaa caaagtttta
      961 ttgtttgctt tgcgcaagga ttctctcatg gcttttttta acctattgtt tgttgcatct
     1021 ctaatttgtt ttggtggtgt tatggggagc tattccagag gttgccgaga ctcccaaaat
     1081 aaattttcaa aagataagga tgagaataat aaaagagcta gtgtttatag atttggtata
     1141 gcatccgcat ttatttgtgt tcctttcata tcatcatttc ttcatgttga ttactcaagt
     1201 ataatatttc ctgtggctga tggtggtgga actaagttca tagaacaaat attgcttctt
     1261 atttctgttt cggggatctc tgcgtatctt gggtacgcat tactggatgg tcttgccaac
     1321 aaagtattaa aagagcaagt agacggtata gataaaaagc aacaagattt ggaggctgaa
     1381 caagatgagt ttaaagatga gcttgatagg agcaaggagc tgatagaaca gcttgaaatg
     1441 gataagaaaa caacaaaatt cgagctagga tactttaaag ccatttcagc tgtggataaa
     1501 gcagaatcaa tgatgtccat tccggatgag gctctttctg ttaagaaaaa actaactgag
     1561 gcattagatg ctgtaacgga atcattgtct cttgttaaaa gagaggatgt agctaaggat
     1621 gactacgaca agctcttagt gcttaaagct tatattttga aaagacttga tcgtattgat
     1681 gatgctctgt caattacgga tgagttactt atgagtaatg aggataaccc tatacttatt
     1741 tacaataagg cttgctatca atatattttg cgtcgttgcc aagctgataa ctccgatatt
     1801 aaggatatga ttcgcagggc tctgactatt aaagttacag atcctgaatt cattcgcagg
     1861 caagaaaaaa taagaaccaa ggtcatagga aataaagata atgatcttga agggttgttt
     1921 actgacgctg agctggagga attaaaggtg gctatcaaat aggcagtggc tagctctatg
     1981 aattccaaaa agatccttga cgatcctttg aggtgcagcg tactctaccc ctcaaacgaa
     2041 aaaaccaccc ggcaaggtgg tttttcgaag gttcagtaac cggcaagttt ctgaaccgag
     2101 gtaactggct tagaggagcg cagtcaccaa aacagttcgt ttagtttagc cttaactggc
     2161 gcataacttc aagactaact cctctaaatc aattaccagt ggctgctgcc aatggcgata
     2221 agtcgtgtct ttccgggttg gactcaagag atagttactg gaacgggcgc agcagtcgga
     2281 ctgaacgggg ggttcgtgca tacagtccag cttggagcga actgccttcc cggagccgag
     2341 tatcaggcat ggaatgagaa aacgcggcca taacagcgga atgacaccgg taaaccgaaa
     2401 ggcaggaaca ggagagcgca cgagggagcc accaggggga aacgcctggt atctttaagt
     2461 cctgtcgggt ttcgccacca ctgatttgag cgtccgtttc cgcgatgctt gtcagggggg
     2521 cggagcctat ggaaaaacag ccgttcggcg gcctttgctt ttctgcctca tatcttggtt
     2581 gcctacgttt ttatgtacac gctcctgccg ctcgccgcag ccgaacggct ggagcgtagc
     2641 gactgagtga gcgaggaagc ggaaaagaga ctagtttgac attgagcact gacgctctga
     2701 ggcttcttat gacaaaacaa cagaaaacag cgctgaacat ggctaaattc atccagaatc
     2761 agtctctgct cctgctggat aagcttaacg agcttgatct cgatgtcgag gccgaccttt
     2821 gtgagaaact ccatgatgat gcggagcatc ttttccgtac actgtcctcg agactggatg
     2881 aattacagga tggtaactga tggccatagt gtctattagt gaagcggcac ggcttgttaa
     2941 ggttagtcgc cccacaattt acaagatgat taacagtggg aagttaagtt acacctctgt
     3001 ggtaaagcac gggaaagcta ttaaagttat tgatacttca gagctaatta gagtgtttgg
     3061 ttctcttgat ggtgtaatcg atactgtaaa atatgatgta aaaagtgacg cagaatctac
     3121 aggtattaac agcgttggtt tacatgattt acaacataga atcgctttac ttgaagctga
     3181 aaacgatggt cttaaagggg ctgttaaggc tcgagatgag catattgatt cccttcgtca
     3241 ggctatgcag cttctggagc acaagcacga accttcttca ccaccccatt ccccgtggtg
     3301 gaaattctgg aaaaaatcct gatcccgcca tgcttccatt ttgctctccg gccattccgg
     3361 ggagttcctg aaccttccca aaaatcgtca gatccctgaa cgctcctcac cactaaaaat
     3421 acccacacac tacgcaaaat taaaattttg cagatagacc tttattttca atcagttatc
     3481 tattttaaat tacgcaattt tattttttgt aaggtgaatc cgagtcgtgg acgactctat
     3541 ggcgaatcgc cgatgacttg cccacgattc atatgtgaat cacgccatat aatcagtacg
     3601 ttatgatgac ttgactctag agtcgacttg ccgggttggt ggctttttga ccatggcgac
     3661 tctagagtca agtcacgagt cgaatcgccg gtgaatcgtg tggtgagtcg tccggcgact
     3721 tgccataatg tgattgctgg tctcgacaaa cccgattcct gaacgtgctg aaaaccggtt
     3781 ttccggctgc gccggcaacg cttcacggcc acgcaataaa ttgcgcaccc gttcaccgtt
     3841 ttcagtctgg tttggtgcgg gttttgagtt gcctggcctg aattcaggct gaaatcccca
     3901 gacagtcagt caagtgcata acgattcatg cccgtaaaac gccctggagc gattttgagg
     3961 cgttttcagg gggtaagacg taggatttaa t
//
