LOCUS       NZ_CP082984             3541 bp    DNA     circular CON 10-FEB-2024
DEFINITION  Klebsiella pneumoniae strain BD-13 plasmid p6-BD-13, complete
            sequence.
ACCESSION   NZ_CP082984
VERSION     NZ_CP082984.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN21016508
            Assembly: GCF_021137635.1
KEYWORDS    RefSeq.
SOURCE      Klebsiella pneumoniae
  ORGANISM  Klebsiella pneumoniae
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Klebsiella/Raoultella group; Klebsiella.
REFERENCE   1  (bases 1 to 3541)
  AUTHORS   Campos-Madueno,E.I. and Endimiani,A.
  TITLE     A collection of hybrid assemblies of carbapenemase-producing
            Klebsiella pneumoniae clinical isolates from Switzerland
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 3541)
  AUTHORS   Campos-Madueno,E.I. and Endimiani,A.
  TITLE     Direct Submission
  JOURNAL   Submitted (02-SEP-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                   :: 662.1413x
            Sequencing Technology :: Illumina NovaSeq and Oxford Nanopore MinION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 02/10/2024 03:12:45
            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)                     :: 5,740
            CDSs (total)                      :: 5,621
            Genes (coding)                    :: 5,468
            CDSs (with protein)               :: 5,468
            Genes (RNA)                       :: 119
            rRNAs                             :: 9, 8, 8 (5S, 16S, 23S)
            complete rRNAs                    :: 9, 8, 8 (5S, 16S, 23S)
            tRNAs                             :: 85
            ncRNAs                            :: 9
            Pseudo Genes (total)              :: 153
            CDSs (without protein)            :: 153
            Pseudo Genes (ambiguous residues) :: 0 of 153
            Pseudo Genes (frameshifted)       :: 61 of 153
            Pseudo Genes (incomplete)         :: 87 of 153
            Pseudo Genes (internal stop)      :: 26 of 153
            Pseudo Genes (multiple problems)  :: 16 of 153
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP082984.1.
            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..3541
                     /organism="Klebsiella pneumoniae"
                     /mol_type="genomic DNA"
                     /strain="BD-13"
                     /host="Homo sapiens"
                     /db_xref="taxon:573"
                     /plasmid="p6-BD-13"
                     /geo_loc_name="Switzerland"
                     /lat_lon="46.9321 N 7.4199 E"
                     /collection_date="2018"
                     /collected_by="Labormedizinisches Zentrum Dr Risch AG,
                     Waldeggstrasse 37, 3097 Liebefeld, Switzerland"
     gene            join(3374..3541,1..234)
                     /locus_tag="K9F21_RS28585"
                     /old_locus_tag="K9F21_28565"
     CDS             join(3374..3541,1..234)
                     /locus_tag="K9F21_RS28585"
                     /old_locus_tag="K9F21_28565"
                     /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_009310048.1"
                     /translation="MARVSISEAARLTGKSRTTLHRLIKAGDLSTCSGERNAKMVDTSE
                     LLRVFGPFEQPKGEHHSGQVSEQRDTASADQSEQVIRHLKQEIEHLNTLLLSKDSHIDS
                     LKQAMLLLENHQAKLTESPAPWWKFWKKS"
                     /name="helix-turn-helix domain-containing protein"
     gene            complement(1044..1481)
                     /locus_tag="K9F21_RS28590"
                     /old_locus_tag="K9F21_28570"
     CDS             complement(1044..1481)
                     /locus_tag="K9F21_RS28590"
                     /old_locus_tag="K9F21_28570"
                     /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_032419556.1"
                     /translation="MTTKNEEFQERLKASLKKANETLILKEKIESDISSILSMLKGITS
                     DSIDFDIFQNSSKIPKYKDCKKIVRIKKNSSMAYPKGFILFGFSINESTGYPVQVETED
                     EAAECTDVDNLKESIVYIIEKRSIEIMKLISEQQEDDDIPF"
                     /name="hypothetical protein"
     gene            complement(1465..2358)
                     /locus_tag="K9F21_RS28595"
                     /old_locus_tag="K9F21_28575"
     CDS             complement(1465..2358)
                     /locus_tag="K9F21_RS28595"
                     /old_locus_tag="K9F21_28575"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000422436.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="endonuclease"
                     /protein_id="WP_032419557.1"
                     /translation="MELNLCWWNIGISPPVKGVKKDKAEAIRLAKHYIKKMSQEKTLDF
                     LGICEISEDEAIDFKPLADKLHLEYLNLSGTVGRIIMDVSIMYEASKLEYIDYKYIIKI
                     QPDDRTLRIAVRVVFKDAVTGNLITFFLSHWPSIRSADEKIREDAAESLRNNVNKILDD
                     HGIESQIICMGDYNTNPYSVAINEKLYATRDYHRIKNKRKLLFNPFWYLLSDKKTNNLG
                     TYHYKSGASNRWFVFDQMLFSSSFIYGGKDCLKLDMNSLDFHRILSDDNQCLDQRFFNT
                     FDHYPIFCRIYHDNQK"
                     /name="endonuclease"
     gene            complement(2656..2769)
                     /locus_tag="K9F21_RS28600"
     CDS             complement(2656..2769)
                     /locus_tag="K9F21_RS28600"
                     /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_072032591.1"
                     /translation="MHEPPVQSDCCALSGNYHLESNPKRHDKAPLAAATGN"
                     /name="replication initiation protein"
     gene            3183..3374
                     /locus_tag="K9F21_RS28605"
                     /old_locus_tag="K9F21_28580"
     CDS             3183..3374
                     /locus_tag="K9F21_RS28605"
                     /old_locus_tag="K9F21_28580"
                     /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          complement(2657..3062)
                     /name="ColRNAI_rep_cluster_1987"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="93.643"
                     /coverage="99.0"
                     /evalue="4.5799999999999997e-172"
ORIGIN
        1 aagggtgaac accattctgg acaggtctct gaacagcgtg atacagcctc tgctgaccag
       61 agtgaacagg tgattcgtca tctgaaacag gagattgaac acctgaatac cttacttttg
      121 tccaaggatt cgcacattga cagcctgaaa caggccatgc tccttcttga aaatcaccag
      181 gcaaaattaa cggaatcccc ggcaccatgg tggaaattct ggaaaaaatc ctgatcctgc
      241 catgcttgag ttttcctctc cggccatccc ggggagttcc tgaaccttcc caaaaatcgc
      301 cagatctctg aacgctcctc acgactaaaa atacccacac actacgcaaa attaaaattt
      361 tgcagatttg tatttaatat cagttgttta ctttcctgaa atttcgtttt ttaaatttta
      421 tttacataga tccgactcta tgacgactcg tcatagagtc cccggcgagt cgtcatagag
      481 tcggtaacga ctcaggacta taaaaacaat gagttaataa cgacccgact ctggacacga
      541 ctccccgttt ggttgttttt tagacgcggc gactctgggt acgactctag tgaagagtcg
      601 ccggtgaatc gtgtggtgag tcgtccggcg acttgccata acgtgattgc cggccgtcga
      661 cgaacccgat tcctgaacgt gctgaaaacc ggttttccgg ctgcgccggc aacgcttcac
      721 ggccacgcaa taaattgcgt ccccgttcac cgttttcgga tgggaagaac gccggaaaca
      781 ggacttaccc tggctgaatg gcgtgaattt tcgcgctatg cacttgcgtg catactcatg
      841 catgccgtaa aaacagagcc tgcgcgtttc tggcgggttt tcgggtggtt tgttgcctgt
      901 tttaccggtt tcccgtcaga aacgccctga ggccgtttta gcggtgcgta caattatggt
      961 cttatgttaa attagttgat tctaagatat atggcacctt ctatgaaaaa gtgccgttga
     1021 taatggcatt acatgctacc tttttaaaaa ggaatgtcat cgtcttcttg ttgctcggat
     1081 attaatttca ttatctctat agatcttttt tctattatgt aaacaattga ttcttttaag
     1141 ttatccacat ctgtacactc tgcggcttcg tcttccgttt ctacctgtac aggatatccg
     1201 gtagactcat ttatgctaaa tccaaataaa atgaaacctt tagggtatgc catgctagag
     1261 tttttcttta ttctgacaat ttttttacaa tctttatatt tgggaatttt cgaactattc
     1321 tgaaaaatat caaagtcaat tgagtcggat gttataccct ttagcattga caaaattgat
     1381 gaaatatctg actctatttt ttcttttaaa attagtgttt cattggcttt ttttagtgat
     1441 gcctttagtc tttcttggaa ctcttcattt ttggttgtca tggtaaatcc tacaaaatat
     1501 tgggtaatga tcaaaagtgt taaaaaatct ttgatctaaa cattggttat catcactaag
     1561 tatacgatga aaatcaaggc tgttcatgtc tagcttaaga caatcttttc ctccgtatat
     1621 aaatgatgat gaaaacaaca tttgatcaaa aacaaaccat ctattcgatg ctcctgattt
     1681 ataatgataa gttcctaagt tattggtctt tttgtctgaa agtaaatacc aaaaagggtt
     1741 aaaaagaagt tttcgtttat tctttattcg atggtaatct ctagtggcgt aaagtttttc
     1801 gtttattgca acagagtaag ggtttgtgtt gtaatcaccc atgcatatta tttgggactc
     1861 aatgccgtgg tcatctagta ttttattcac attgttgcgc agtgactcgg cagcgtcctc
     1921 tcgaatcttt tcatctgcgc ttcttatgga tggccagtgt gataaaaaga atgttattag
     1981 atttcctgtt actgcatcct taaaaacaac tctgacagca atacgcaaag ttctatcatc
     2041 tggttgtatt ttaattatat atttataatc tatgtactca agttttgatg cttcgtacat
     2101 tatggataca tccataatta tccgaccaac agtccctgat aaattcaagt attcaagatg
     2161 tagtttatca gccaaaggtt taaaatctat agcctcatct tctgatattt cacagatacc
     2221 caaaaaatcc aatgtttttt cttgagacat tttttttata tagtgcttgg ccaatctaat
     2281 agcctcagcc ttgtctttct tcacgccttt tacaggtggt gatattccaa tattccacca
     2341 acataaattc aattccatgg tgtttctttc ttaatgcatt gtattcattg ggtttattgt
     2401 attgcttttg atgtgggggt taaacatttt atttatctgt ttgttgataa atggtgttgc
     2461 gctacccctt ttaaggcgtt atcttcttgg ctggaaatga aaaaaccgcc ttgcagggcg
     2521 gttttttcaa gggttcaaat aacttgcagg tcttttgaac ctaggtaact ggctagtaga
     2581 ggagcgcagt caccaaaact tgttctttca gtgtagcctt aactgaccca taacttcaag
     2641 actaactcct ctaaatcagt taccagtggc tgctgccagt ggcgctttgt cgtgtctttt
     2701 cgggttggac tcaagatgat agttaccgga taaggcgcag cagtcggact gaacgggggg
     2761 ttcgtgcata cagtccagct tggagcgaac tgcctacccg gaactgagtg tcaggcgtgg
     2821 aatgagaaaa acgcggccat aacagcggaa tgacaccggt aaaccgaatg gcaggaacag
     2881 gagagcgcac gagggagcca tcagggggaa acgcctggta tctttatagt cctgtcgggt
     2941 ttcgccacca ctgatttgag cgtccgcttc ggtgatgctt gtcagggggg cggagcctat
     3001 ggaaaaacgg ccgctttgcg gcctttcctt cttccccatt tgaccgctcg gtcttctcga
     3061 gcttttatac gcatgctcct gccgctcgcc gcagccgaac gaccggagcg tagcgactga
     3121 gtgagcgagg aagcggaaaa gagactgttc ttacactgag cactgacgct ctgaggcttc
     3181 ttatgacgaa acaacagaaa acagcgctga acatggctaa attcatccag aatcagtctc
     3241 tgctcctgct ggagaagctt aacgagcttg atcttgatgt cgaggccgac ctttgtgaga
     3301 aactccacga tgatgcggag catcttttcc gtacactgtc ctcgagactg gatgcattac
     3361 aggatggtaa ctgatggcca gagtgtctat tagtgaggct gcccgactga cgggtaagag
     3421 tagaacaaca ctgcacaggt taattaaagc aggtgacctg tccacctgta gcggtgaacg
     3481 aaatgcaaaa atggtagata cttcagagct tttacgtgtc tttggtccct ttgaacaacc
     3541 g
//
