LOCUS       NZ_CP082974             3541 bp    DNA     circular CON 10-FEB-2024
DEFINITION  Klebsiella pneumoniae strain BD-41 plasmid p7-BD-41, complete
            sequence.
ACCESSION   NZ_CP082974
VERSION     NZ_CP082974.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN21016516
            Assembly: GCF_021135615.1
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  JOURNAL   Unpublished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                   :: 528.8007x
            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 02:48:12
            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)                     :: 5,786
            CDSs (total)                      :: 5,665
            Genes (coding)                    :: 5,500
            CDSs (with protein)               :: 5,500
            Genes (RNA)                       :: 121
            rRNAs                             :: 9, 8, 8 (5S, 16S, 23S)
            complete rRNAs                    :: 9, 8, 8 (5S, 16S, 23S)
            tRNAs                             :: 87
            ncRNAs                            :: 9
            Pseudo Genes (total)              :: 165
            CDSs (without protein)            :: 165
            Pseudo Genes (ambiguous residues) :: 0 of 165
            Pseudo Genes (frameshifted)       :: 68 of 165
            Pseudo Genes (incomplete)         :: 96 of 165
            Pseudo Genes (internal stop)      :: 27 of 165
            Pseudo Genes (multiple problems)  :: 20 of 165
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP082974.1.
            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-41"
                     /host="Homo sapiens"
                     /db_xref="taxon:573"
                     /plasmid="p7-BD-41"
                     /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            complement(join(3365..3541,1..225))
                     /locus_tag="K9F23_RS28825"
                     /old_locus_tag="K9F23_28770"
     CDS             complement(join(3365..3541,1..225))
                     /locus_tag="K9F23_RS28825"
                     /old_locus_tag="K9F23_28770"
                     /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(225..416)
                     /locus_tag="K9F23_RS28830"
                     /old_locus_tag="K9F23_28775"
     CDS             complement(225..416)
                     /locus_tag="K9F23_RS28830"
                     /old_locus_tag="K9F23_28775"
                     /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"
     gene            830..943
                     /locus_tag="K9F23_RS28835"
     CDS             830..943
                     /locus_tag="K9F23_RS28835"
                     /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            1241..2134
                     /locus_tag="K9F23_RS28840"
                     /old_locus_tag="K9F23_28780"
     CDS             1241..2134
                     /locus_tag="K9F23_RS28840"
                     /old_locus_tag="K9F23_28780"
                     /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            2118..2555
                     /locus_tag="K9F23_RS28845"
                     /old_locus_tag="K9F23_28785"
     CDS             2118..2555
                     /locus_tag="K9F23_RS28845"
                     /old_locus_tag="K9F23_28785"
                     /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"
     Typing          538..943
                     /name="ColRNAI_rep_cluster_1987"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="93.643"
                     /coverage="99.0"
                     /evalue="4.5799999999999997e-172"
ORIGIN
        1 gtcagcagag gctgtatcac gctgttcaga gacctgtcca gaatggtgtt cacccttcgg
       61 ttgttcaaag ggaccaaaga cacgtaaaag ctctgaagta tctaccattt ttgcatttcg
      121 ttcaccgcta caggtggaca ggtcacctgc tttaattaac ctgtgcagtg ttgttctact
      181 cttacccgtc agtcgggcag cctcactaat agacactctg gccatcagtt accatcctgt
      241 aatgcatcca gtctcgagga cagtgtacgg aaaagatgct ccgcatcatc gtggagtttc
      301 tcacaaaggt cggcctcgac atcaagatca agctcgttaa gcttctccag caggagcaga
      361 gactgattct ggatgaattt agccatgttc agcgctgttt tctgttgttt cgtcataaga
      421 agcctcagag cgtcagtgct cagtgtaaga acagtctctt ttccgcttcc tcgctcactc
      481 agtcgctacg ctccggtcgt tcggctgcgg cgagcggcag gagcatgcgt ataaaagctc
      541 gagaagaccg agcggtcaaa tggggaagaa ggaaaggccg caaagcggcc gtttttccat
      601 aggctccgcc cccctgacaa gcatcaccga agcggacgct caaatcagtg gtggcgaaac
      661 ccgacaggac tataaagata ccaggcgttt ccccctgatg gctccctcgt gcgctctcct
      721 gttcctgcca ttcggtttac cggtgtcatt ccgctgttat ggccgcgttt ttctcattcc
      781 acgcctgaca ctcagttccg ggtaggcagt tcgctccaag ctggactgta tgcacgaacc
      841 ccccgttcag tccgactgct gcgccttatc cggtaactat catcttgagt ccaacccgaa
      901 aagacacgac aaagcgccac tggcagcagc cactggtaac tgatttagag gagttagtct
      961 tgaagttatg ggtcagttaa ggctacactg aaagaacaag ttttggtgac tgcgctcctc
     1021 tactagccag ttacctaggt tcaaaagacc tgcaagttat ttgaaccctt gaaaaaaccg
     1081 ccctgcaagg cggttttttc atttccagcc aagaagataa cgccttaaaa ggggtagcgc
     1141 aacaccattt atcaacaaac agataaataa aatgtttaac ccccacatca aaagcaatac
     1201 aataaaccca atgaatacaa tgcattaaga aagaaacacc atggaattga atttatgttg
     1261 gtggaatatt ggaatatcac cacctgtaaa aggcgtgaag aaagacaagg ctgaggctat
     1321 tagattggcc aagcactata taaaaaaaat gtctcaagaa aaaacattgg attttttggg
     1381 tatctgtgaa atatcagaag atgaggctat agattttaaa cctttggctg ataaactaca
     1441 tcttgaatac ttgaatttat cagggactgt tggtcggata attatggatg tatccataat
     1501 gtacgaagca tcaaaacttg agtacataga ttataaatat ataattaaaa tacaaccaga
     1561 tgatagaact ttgcgtattg ctgtcagagt tgtttttaag gatgcagtaa caggaaatct
     1621 aataacattc tttttatcac actggccatc cataagaagc gcagatgaaa agattcgaga
     1681 ggacgctgcc gagtcactgc gcaacaatgt gaataaaata ctagatgacc acggcattga
     1741 gtcccaaata atatgcatgg gtgattacaa cacaaaccct tactctgttg caataaacga
     1801 aaaactttac gccactagag attaccatcg aataaagaat aaacgaaaac ttctttttaa
     1861 ccctttttgg tatttacttt cagacaaaaa gaccaataac ttaggaactt atcattataa
     1921 atcaggagca tcgaatagat ggtttgtttt tgatcaaatg ttgttttcat catcatttat
     1981 atacggagga aaagattgtc ttaagctaga catgaacagc cttgattttc atcgtatact
     2041 tagtgatgat aaccaatgtt tagatcaaag attttttaac acttttgatc attacccaat
     2101 attttgtagg atttaccatg acaaccaaaa atgaagagtt ccaagaaaga ctaaaggcat
     2161 cactaaaaaa agccaatgaa acactaattt taaaagaaaa aatagagtca gatatttcat
     2221 caattttgtc aatgctaaag ggtataacat ccgactcaat tgactttgat atttttcaga
     2281 atagttcgaa aattcccaaa tataaagatt gtaaaaaaat tgtcagaata aagaaaaact
     2341 ctagcatggc ataccctaaa ggtttcattt tatttggatt tagcataaat gagtctaccg
     2401 gatatcctgt acaggtagaa acggaagacg aagccgcaga gtgtacagat gtggataact
     2461 taaaagaatc aattgtttac ataatagaaa aaagatctat agagataatg aaattaatat
     2521 ccgagcaaca agaagacgat gacattcctt tttaaaaagg tagcatgtaa tgccattatc
     2581 aacggcactt tttcatagaa ggtgccatat atcttagaat caactaattt aacataagac
     2641 cataattgta cgcaccgcta aaacggcctc agggcgtttc tgacgggaaa ccggtaaaac
     2701 aggcaacaaa ccacccgaaa acccgccaga aacgcgcagg ctctgttttt acggcatgca
     2761 tgagtatgca cgcaagtgca tagcgcgaaa attcacgcca ttcagccagg gtaagtcctg
     2821 tttccggcgt tcttcccatc cgaaaacggt gaacggggac gcaatttatt gcgtggccgt
     2881 gaagcgttgc cggcgcagcc ggaaaaccgg ttttcagcac gttcaggaat cgggttcgtc
     2941 gacggccggc aatcacgtta tggcaagtcg ccggacgact caccacacga ttcaccggcg
     3001 actcttcact agagtcgtac ccagagtcgc cgcgtctaaa aaacaaccaa acggggagtc
     3061 gtgtccagag tcgggtcgtt attaactcat tgtttttata gtcctgagtc gttaccgact
     3121 ctatgacgac tcgccgggga ctctatgacg agtcgtcata gagtcggatc tatgtaaata
     3181 aaatttaaaa aacgaaattt caggaaagta aacaactgat attaaataca aatctgcaaa
     3241 attttaattt tgcgtagtgt gtgggtattt ttagtcgtga ggagcgttca gagatctggc
     3301 gatttttggg aaggttcagg aactccccgg gatggccgga gaggaaaact caagcatggc
     3361 aggatcagga ttttttccag aatttccacc atggtgccgg ggattccgtt aattttgcct
     3421 ggtgattttc aagaaggagc atggcctgtt tcaggctgtc aatgtgcgaa tccttggaca
     3481 aaagtaaggt attcaggtgt tcaatctcct gtttcagatg acgaatcacc tgttcactct
     3541 g
//
