LOCUS       NZ_CP082982             5359 bp    DNA     circular CON 10-FEB-2024
DEFINITION  Klebsiella pneumoniae strain BD-13 plasmid p4-BD-13, complete
            sequence.
ACCESSION   NZ_CP082982
VERSION     NZ_CP082982.1
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 5359)
  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  JOURNAL   Unpublished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 5359)
  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
            CP082982.1.
            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..5359
                     /organism="Klebsiella pneumoniae"
                     /mol_type="genomic DNA"
                     /strain="BD-13"
                     /host="Homo sapiens"
                     /db_xref="taxon:573"
                     /plasmid="p4-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            126..611
                     /locus_tag="K9F21_RS28535"
                     /old_locus_tag="K9F21_28505"
     CDS             126..611
                     /locus_tag="K9F21_RS28535"
                     /old_locus_tag="K9F21_28505"
                     /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="MbeB family mobilization protein"
                     /protein_id="WP_055314654.1"
                     /translation="MSSLLALAKDLEQQSKAQQQSTGEMLKAAFSEHEKSVKAELSASA
                     KRISDAISAHEQGMTAAMQSNRLSVLRMVGRTWLTITLVSVLLIAMSGSILWWQGQQIT
                     GNYQTIRAQERTQAMLSEKNHGVQLSLCGEKKLSCVKVNPKAGAYGEEGNWMVLERK"
                     /name="MbeB family mobilization protein"
     gene            615..827
                     /locus_tag="K9F21_RS28540"
                     /old_locus_tag="K9F21_28510"
     CDS             615..827
                     /locus_tag="K9F21_RS28540"
                     /old_locus_tag="K9F21_28510"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000137423.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MbeD family mobilization/exclusion protein"
                     /protein_id="WP_000137423.1"
                     /translation="MTELEKQLLTALEQLHQDYSQRLDEWESAFAEWQKMSGLMQRENA
                     ALNERVTRLSQQVANLSRQLQRLSQ"
                     /name="MbeD family mobilization/exclusion protein"
     gene            complement(1377..1640)
                     /locus_tag="K9F21_RS28545"
                     /old_locus_tag="K9F21_28515"
     CDS             complement(1377..1640)
                     /locus_tag="K9F21_RS28545"
                     /old_locus_tag="K9F21_28515"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_010891192.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_054175658.1"
                     /translation="MAAYTSETEKFLQSVSSDQTWWKSRYNPGDSVPHSGIYRCTVCGK
                     EITSNGSDPFPPQNHHQHSQQQAIKWQLIVRTDTKGDRFGIK"
                     /name="hypothetical protein"
     gene            complement(2058..2474)
                     /locus_tag="K9F21_RS28550"
                     /old_locus_tag="K9F21_28520"
     CDS             complement(2058..2474)
                     /locus_tag="K9F21_RS28550"
                     /old_locus_tag="K9F21_28520"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001283459.1"
                     /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_032419562.1"
                     /translation="MSDQKNNLDIQKQTLESKWGKEALSMGWSAIPTSLFFLQGALNMT
                     PTTFNVLLHLIIHWWKPYDWPHPSQESIAVRMGVSSRTVQRSLQELENYGLLTKIRTSK
                     DNPKYKGRNIYDMSLLVKSLNILTPDLNAKLNEK"
                     /name="helix-turn-helix domain-containing protein"
     gene            2822..3496
                     /locus_tag="K9F21_RS28555"
                     /old_locus_tag="K9F21_28525"
     CDS             2822..3496
                     /locus_tag="K9F21_RS28555"
                     /old_locus_tag="K9F21_28525"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001259273.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="NYN domain-containing protein"
                     /protein_id="WP_032419561.1"
                     /translation="MRTIVYVDGFNFYHGLVKRSGYKWLDLYKLFEEQLLPIRARESQL
                     IQVKFFTAEIKAKFASRGELAHQAQQAYHRALVQIYGDKLQIIKGYYSERQECAMTFNE
                     GHPPSKTDRTTVWKLEEKQTDVRMALEMYRDAIRGEVEQLVLCTNDSDMIPPIEMIKAD
                     RPELKIGIVVPREQDTSRVISNLASLGDWSLPYVSYEALRLALLPDKVPTRRKPILKPN
                     HW"
                     /name="NYN domain-containing protein"
     gene            4487..4807
                     /locus_tag="K9F21_RS28560"
                     /old_locus_tag="K9F21_28530"
     CDS             4487..4807
                     /locus_tag="K9F21_RS28560"
                     /old_locus_tag="K9F21_28530"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000957083.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MobC family plasmid mobilization relaxosome
                     protein"
                     /protein_id="WP_042863636.1"
                     /translation="MLTMWVTEDEHRRLLERCDGRQLAAWMRQTCLDEKPARAGRLPSI
                     SPALLRQLAGMGNNLNQIARKVNAGGAGHDRVQIVAALMAIDAGLERLRHAVLEKGGDD
                     DR"
                     /name="MobC family plasmid mobilization relaxosome protein"
     Typing          4199..4379
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="87.978"
                     /coverage="83.0"
                     /evalue="2.08e-53"
     Typing          complement(3739..4249)
                     /name="ColRNAI_rep_cluster_1987"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="93.359"
                     /coverage="98.0"
                     /evalue="0.0"
     Typing          3..943
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="97.452"
                     /coverage="99.0"
                     /evalue="0.0"
     Typing          4771..5357
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="91.837"
                     /coverage="95.0"
                     /evalue="2.9e-110"
ORIGIN
        1 aacgcgcgag gacgtcacag gggcgctcac agcggcaggt tttgaggtgg tccgcaccac
       61 aaaaaacagt atcagcattg ccgacccgga cggggggcga aacatccgac tgaagggagc
      121 catttatgag cagtctttta gcgctggcga aggacttgga gcagcaatcg aaagcgcagc
      181 agcagagtac cggcgagatg ctgaaagccg cattcagcga gcacgagaaa tctgtaaaag
      241 cggaactgag cgcaagcgcg aagagaatca gcgacgccat cagcgcccac gagcagggta
      301 tgaccgcggc gatgcagtcg aaccgcctga gcgtgctgcg tatggtcggc cggacgtggc
      361 tgaccatcac cctggtctcg gtactgctga tcgccatgag cgggagcatt ctgtggtggc
      421 aggggcagca gatcaccggg aattaccaga ctatccgggc gcaggagcgg acgcaggcca
      481 tgttgtcgga gaaaaaccac ggcgttcagc tgtcgctctg cggggagaag aaactgtcct
      541 gcgtcaaagt gaacccgaaa gcgggagctt acggggagga agggaactgg atggtactgg
      601 agaggaaata gcccatgacg gaactggaaa aacagttgct gaccgcatta gagcagctac
      661 atcaggacta ctcgcaaagg ctggacgagt gggagagcgc cttcgcggaa tggcagaaga
      721 tgtctggtct tatgcaacgg gagaacgcgg cgctgaacga gcgcgtcacg cgcttgagtc
      781 agcaggtggc gaacttgagc aggcagttac agcgtttgag ccagtagtgc agcggcatga
      841 aatggcggtg gccgccgaac gggcatacga gcagcgacag cacgaaaaag agctggcgga
      901 agcccgttcc cgtcagcgga gttatgacgg tccgacactg ggctgaacag tatcatccgg
      961 tgacaggccg cacgaagaag ggctcttatt tctcccgcta aataggttcg tgatcaaaaa
     1021 gagcacggcc tatacctagg gggaattatg aaattgctta acgtcattga agctgtactt
     1081 aactgcctgt atctggcgac cgagctgtgg gactggctgg agaagcattt tcctgttttt
     1141 aaggcgttca tccggattct ggcctgaaat cagactgtat gcatctggct gcatgaccat
     1201 gcagccgggg aaaatttatc tgtcacgaac ggggcggtgt atcgggtggt ttgttgccgg
     1261 ttttacctga ctgccgtccc gtttgtggcg aacctgtccg gagcggtgcg ggcaagggat
     1321 gttatggtaa atatcttcga gcttcaggta caaaaaaagc cccggagggc tctcaatcat
     1381 ttgattccga aacggtcacc tttagtgtcc gttctgacaa tcaattgcca tttgattgct
     1441 tgttgctgac tgtgctgatg atggttttgc ggcgggaacg ggtcgctgcc gttactggtg
     1501 atctcttttc cgcagacggt acatcgataa attccagaat ggggaacgct gtctcctgga
     1561 ttatatcgtg acttccacca tgtttgatcg ctactgacgc tttgtaaaaa cttctctgtt
     1621 tcgctggtat atgcagccat ttagctttcc ttttctgaat ttatagggca gagatagaaa
     1681 agccgcccgc tggggcggct tttcgttgcc agtctaaata tcaagcatat tgggttaaca
     1741 tccaggttac agcctttcct gcgtacggag gcattacatt accttttgct atcggggctg
     1801 tagtggaagg ggttcctacg actttccaga caccactttc aggacacttt tgtccggtag
     1861 aagcagtcgt accaattggt gctttagaca tgctaattcc tctttttgtg ttttgtccgt
     1921 attgctgttt gtgtagcgat actgatgttt agtttagaaa ttagctttca atagggagct
     1981 gttgtcattt tctagaaatg tgatgctgaa caccttttgt acagtgatgt gcgcgctttg
     2041 gctgtcggaa tttttggtta cttttcgttt agtttggcgt tgaggtctgg cgtaagaatg
     2101 tttagtgact taactaaaag agacatatcg taaatgtttc gccctttgta cttagggttg
     2161 tccttgcttg tacgaatttt tgtaagcaat ccgtaatttt caagttcttg gagtgagcgt
     2221 tgaactgttc ttgatgaaac tcccattcta accgcgatgc tctcttgaga tggatgtggc
     2281 caatcatagg gtttccacca gtggataatt agatgaagta gcacattgaa tgttgtgggg
     2341 gtcatattga gtgcgccctg caggaagaaa agggatgtag gaatggctga ccatcccatg
     2401 cttaacgctt ccttccccca tttagactca agtgtctgtt tttgaatgtc taaattattt
     2461 ttttgatctg acatatacca acctgctaag ctgaagtctt cttagaagac ttcagcttag
     2521 caggttggta aattaattca tataattagt acgacaccag tgcgcttata atatcattat
     2581 atttaactat acttaatcta cactcacctc ttggtagcgc gattaagtta cgcagctccc
     2641 ttgaggctct aaacctccct ttaggtgggc agcgattaag ttacgcgtct tccttcagga
     2701 gcttgaaacc gccctctcgg ttagttttaa ccctgaggta ctacaactta aactgtttgc
     2761 taacgttagt ttttgttgtt aaaaccgccc ttagaggcgg tttttttatg cgcgaaataa
     2821 aatgagaaca atagtttacg tagatgggtt caatttttat cacggattgg ttaagcgttc
     2881 gggatataag tggttagacc tttataagct ctttgaagaa caactgcttc cgataagagc
     2941 acgagaatca cagttgattc aggtgaagtt ctttactgct gagatcaagg caaagtttgc
     3001 ttctcggggt gaattggcgc accaagctca gcaagcctac catcgagcat tagtacagat
     3061 ctatggcgat aagctacaga taataaaagg ttattactca gagcgtcagg aatgtgcaat
     3121 gacctttaat gaggggcatc ctccatcaaa aacggataga acaacggtct ggaagttaga
     3181 agaaaagcag acagacgtta gaatggcttt agaaatgtat cgcgatgcga ttcgtggtga
     3241 agtagaacaa ttggttctct gcactaacga ctcagatatg ataccgccaa tagaaatgat
     3301 aaaagctgat cggcctgagt taaaaatagg aatcgtagtg ccaagggaac aggatactag
     3361 tcgagtgatt agtaatctgg ctagtttagg ggattggagc ttgccatatg tatcctatga
     3421 agccttaaga ttagctttat tgccagataa agtccccact aggcggaagc caatactgaa
     3481 gccaaatcac tggtaaacag ccggatcttc ttgtgatcct tttactctcg tcgtaatctc
     3541 atgccctgca aacaaaaaaa ccaccgctac caacggtggt tcgtttgccg gaatcaagag
     3601 ctaccaactc tttttcccga aggtaactgg ctttcacgga gcgcagatac caaaactgtc
     3661 cttccagtgt agccgcagtc aggccaccac ttcaagaact ctgtagaagc actctactac
     3721 tctgctccgt gaatcctgtt accagtggct gctgccagtg gcgtttttgc gtgtctttcc
     3781 ggattggact caagacgata gttaccggaa aaggcgcagc ggtcggactg aacggggggt
     3841 tcgtgcatac agtccagctt ggagcgaact gcctacccgg aactgagtgt caggcgtgga
     3901 atgagacaaa cgcggccata acagcggaat gacaccggta aaccgaaagg caggaacagg
     3961 agagcgcacg agggagccac cagggggaaa cgcctggtat ctttatagtc ctgtcgggtt
     4021 tcgccaccac tgatttgagc gtcagatttc gtgatgcttg tcaggggggc ggagcctatg
     4081 gaaaaacggc agcgccgcat ccttttcccg ccctgcttgt catgtcatat gcctttgctc
     4141 ttatccgtgt gtgcgtaacg cccgccgcag ccgaacggca ggagcggaag cgaccgagtg
     4201 agcgaggagg cgtcatatca ccgtaacctc cattttctcc tgtacgccct gtagctgcat
     4261 tttccccctg tcacatgaag cactttcata aagtgttact cctccgtaac atattgagcc
     4321 agtatacact ccgctagcgc tacgtgactg gttcagggct gcgccccgaa acccgctaaa
     4381 agccactgac gcgcctgcgg cttgtccaac accgtgccga ccgggaaaca tttcccgccc
     4441 gtcccggtgt tctcaggagg ctactctggc agacaaacgc aacaagatgc tcacgatgtg
     4501 ggtgacggaa gacgaacacc ggcggctgct cgagcggtgc gacggcaggc agctggcggc
     4561 gtggatgcgt cagacctgcc tcgatgagaa gccggcgcgt gccggcagac tgccgtcgat
     4621 atcgccggcg ctgctgcgcc agcttgccgg tatggggaac aacctgaacc agatcgcccg
     4681 gaaagtgaat gccggtggtg ccggtcatga ccgggtgcag attgtggccg ccctgatggc
     4741 aatcgacgcg ggactggagc ggctgcggca tgcggtgctg gaaaaagggg gggatgatga
     4801 tcgttaaatt tcacccccgg gggcgcggtg gtggtgccgg tccggtggat tacctgctgg
     4861 gaaaagaccg gcagcgcgag ggggcgaccg tgctgcaggg aaaaccggag gaagtccggg
     4921 agcttatcga tgcctcgccg tatgcgaaaa agtacacctc cggcgtgctg tcgttcgcgg
     4981 aggctgaact gccgcccggg cagcgggagc agatcatggc cagctttgag cgggttctga
     5041 tgcccgggct cgataaagac cagtacagca ttctgtgggt ggagcatacc gacaagggga
     5101 ggctggagct gaatttcctg atccccaaca ctgaactgct gaccgggaaa cgcctgcagc
     5161 cgtactacga tcgcgccgac cggccgcgca tcgatgcctg gcagaccgtg gtgaacggca
     5221 gactggggct gcatgatcca aacgccccgg agaaccggcg gttactggtc acgccgtccg
     5281 cactgccgga aacgaagctg gaagccgctc aggcgattac acgggggttg ctggccttag
     5341 cctcatccgg ggagctcaa
//
