LOCUS       NZ_CP099746             4091 bp    DNA     circular CON 29-SEP-2023
DEFINITION  Klebsiella pneumoniae strain 503666-2-2019 plasmid p503666-2-2019d,
            complete sequence.
ACCESSION   NZ_CP099746
VERSION     NZ_CP099746.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN29187370
            Assembly: GCF_025232415.1
KEYWORDS    RefSeq.
SOURCE      Klebsiella pneumoniae
  ORGANISM  Klebsiella pneumoniae
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Klebsiella/Raoultella group; Klebsiella.
REFERENCE   1  (bases 1 to 4091)
  AUTHORS   Fernandez,J.E., Seth-Smith,H.M.B., Nordmann,P., Egli,A.,
            Endimiani,A. and Perreten,V.
  TITLE     Intra and inter-species spread of a novel conjugative
            multidrug-resistant IncC plasmid co-harbouring blaOXA-181 and armA
            in a cystic fibrosis patient
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 4091)
  AUTHORS   Fernandez,J.E. and Perreten,V.
  TITLE     Direct Submission
  JOURNAL   Submitted (21-JUN-2022) Institute of Veterinary Bacteriology,
            University of Bern, Laenggassstrasse 122, Bern 3012, Switzerland
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Date                     :: MAY-2022
            Assembly Method                   :: Unicycler v. 0.4.9b
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 300x
            Sequencing Technology :: Illumina NextSeq; Oxford Nanopore MinION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 09/29/2023 07:33:01
            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)                     :: 5,622
            CDSs (total)                      :: 5,501
            Genes (coding)                    :: 5,368
            CDSs (with protein)               :: 5,368
            Genes (RNA)                       :: 121
            rRNAs                             :: 9, 8, 8 (5S, 16S, 23S)
            complete rRNAs                    :: 9, 8, 8 (5S, 16S, 23S)
            tRNAs                             :: 86
            ncRNAs                            :: 10
            Pseudo Genes (total)              :: 133
            CDSs (without protein)            :: 133
            Pseudo Genes (ambiguous residues) :: 0 of 133
            Pseudo Genes (frameshifted)       :: 56 of 133
            Pseudo Genes (incomplete)         :: 79 of 133
            Pseudo Genes (internal stop)      :: 22 of 133
            Pseudo Genes (multiple problems)  :: 20 of 133
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP099746.1.
            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..4091
                     /organism="Klebsiella pneumoniae"
                     /mol_type="genomic DNA"
                     /strain="503666-2-2019"
                     /isolation_source="sputum"
                     /host="Homo sapiens"
                     /db_xref="taxon:573"
                     /plasmid="p503666-2-2019d"
                     /geo_loc_name="Switzerland: Basel"
                     /lat_lon="47.5617 N 7.58339 E"
                     /collection_date="2019"
                     /collected_by="University Hospital Basel"
     gene            complement(835..1236)
                     /locus_tag="NHF44_RS27065"
                     /old_locus_tag="NHF44_27050"
     CDS             complement(835..1236)
                     /locus_tag="NHF44_RS27065"
                     /old_locus_tag="NHF44_27050"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_009310048.1"
                     /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_060588945.1"
                     /translation="MARVSISEAARLTGKSRTTLHRLIKAGDLSTCSGERNAKMVDTSE
                     LLRVFGPFEQSKSEHHSGQVSEQRDTASADQSEQVIRHLKQEIEHLNTLLLSKDSHIDS
                     LKQAMLLLENHQAKLTESPAPWWKFWKKS"
                     /name="helix-turn-helix domain-containing protein"
     gene            complement(1236..1427)
                     /locus_tag="NHF44_RS27070"
                     /old_locus_tag="NHF44_27055"
     CDS             complement(1236..1427)
                     /locus_tag="NHF44_RS27070"
                     /old_locus_tag="NHF44_27055"
                     /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_032421723.1"
                     /translation="MTKQQKTALNMAKFIQNQSLLLLEKLNELDLDAEADLCEKLHDDA
                     EHLFRTLSSRLDELQDGN"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            complement(1909..2058)
                     /locus_tag="NHF44_RS27075"
                     /old_locus_tag="NHF44_27060"
     CDS             complement(1909..2058)
                     /locus_tag="NHF44_RS27075"
                     /old_locus_tag="NHF44_27060"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_017880354.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_017880354.1"
                     /translation="MPSEYDEQLDSTDTQLPGEYDLFDLMAQVTEENLHAPVDSGPPVG
                     REAL"
                     /name="hypothetical protein"
     gene            3285..3605
                     /locus_tag="NHF44_RS27080"
                     /old_locus_tag="NHF44_27065"
     CDS             3285..3605
                     /locus_tag="NHF44_RS27080"
                     /old_locus_tag="NHF44_27065"
                     /inference="COORDINATES: protein motif:HMM:NF017757.3"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="type II toxin-antitoxin system RelE/ParE family
                     toxin"
                     /protein_id="WP_048333942.1"
                     /translation="MAQLELKMEKVVEKEFRALENRKVQEAFAVDLEMIMNGLKPLSSS
                     KPLNGLGKGVFELKKNGRPAYRCVYVVKNNTLYVLHVYSKTSDGTPKHHEDTIKKRFKS
                     VK"
                     /name="type II toxin-antitoxin system RelE/ParE family
                     toxin"
     gene            complement(3631..3951)
                     /locus_tag="NHF44_RS27085"
                     /old_locus_tag="NHF44_27070"
     CDS             complement(3631..3951)
                     /locus_tag="NHF44_RS27085"
                     /old_locus_tag="NHF44_27070"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_017134632.1"
                     /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 transcriptional regulator"
                     /protein_id="WP_048333940.1"
                     /translation="MLNKFSSPFELFAKDAVELNMLSLKSKLLIIIAEMIRGEGWSQAA
                     AADKLGVSQPRVSNLMNGHVSKFAIDTLLEMLCRIGFVVDVTFRPHDEESPLHVSVKKA
                     VV"
                     /name="helix-turn-helix transcriptional regulator"
     Typing          2214..2738
                     /name="ColRNAI_rep_cluster_1987"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="89.225"
                     /coverage="99.0"
                     /evalue="0.0"
ORIGIN
        1 gaagacttgt tatagttcgc ttcacttcat cccgtcaacc cctttcgtca acaattttgt
       61 agtgtatgtt ggcaaaaact atcgtgcttt agaacggatt taccataaca tccgttgcgt
      121 gcaccgcctc agaggccctc agcgcgtttc tgcgccctcc cgcctgtttc cggcaccttt
      181 ccctgtccat atcgtgaaaa aacgcgcctg atgattctgg cgcgactgca tggctatgca
      241 cggacatacc tggccgggat tttagcggct aaaatccgat gaacgccctg aaagccacca
      301 cgaaccaccc cgataacggt gaacggatgc gcaatttatt gcgtggccgt gaggcgttgc
      361 cggcgcagcc ggaaaacccg ttttcagcac gttcaggaat ccggttcagc gacagccggc
      421 aatgacgtga tggcaagtca ccggacgact tagcacacga ttcaccggcg attcgactcg
      481 ggacttgact ctagagtcac cccggtcaaa aaaaacgcca aatcgacgat tcgactctag
      541 agtcaagtcg tcataagtta ctgatagtgt ggagtgagtc gtcgatgact ctatgacgag
      601 tcgtcggcaa gtcgtacacg aatcgccgac gacttggatt gaccttacag aaggtaatac
      661 tgcgtaattt aataacaacc aactaactga tattaatgag ttatctgcaa aaatttaatt
      721 ttgcgtgggg tgtggatatt tttagagtga ggagcgttca gagatctggc gatttttggg
      781 aaggttcagg aactccccgg gatggccgga gaggaaaact caagcatggc gggatcagga
      841 ttttttccag aatttccacc atggcgccgg ggattcagtt aattttgcct ggtgattttc
      901 aagaaggagc atggcctgtt tcaggctgtc aatgtgcgaa tccttggaca aaagtaaggt
      961 gttcaggtgt tcaatctcct gtttcagatg acgaatcacc tgttcactct ggtcagcaga
     1021 ggctgtatca cgctgttcag agacctgtcc agaatgatgt tcactcttcg attgttcaaa
     1081 gggcccaaag acacgtaaaa gctctgaagt atctaccatt tttgcattgc gttcaccgct
     1141 acaggtggac aggtcacctg ctttaattaa cctgtgcagt gttgttctac tcttacccgt
     1201 cagtcgggcg gcctcactaa tagacactct ggccatcagt taccatcctg taattcatcc
     1261 agtctcgagg acagtgtacg gaaaagatgc tccgcatcat cgtgtagttt ctcacaaagg
     1321 tcggcctcag catcgagatc aagctcgtta agcttctcca gcaggagcag agactgattc
     1381 tggatgaatt tagccatgtt cagcgctgtt ttctgttgtt tcgtcataag ggacctcaga
     1441 gcatcaatgc tcagtgtaaa accggtaagg gggtcggatg tacgaatggt tcagagaacg
     1501 gatctgaggt aatcctgtag ttattttgta gtttatctgt agtcatcgca ctaaaaatca
     1561 ggattaagtc atcagctttt gtagtctttc tgtagtttac ctgtagtccg gaaaaataat
     1621 ccgttcatgc gagcatgaac gaggtcgtta atgacgtttt tttgtcaccg acgcccctta
     1681 acctccgcag atcacccggc cagaatgata attttttggc ccttaaatgg tcatacacct
     1741 aacgcagccg cgattttcat cgcaactgca tgaattaaaa agtaaaaact gaaatctccg
     1801 tttatttatg taatacgcaa cgtattacaa tcacctgtaa ttacatgaaa ataaagaaat
     1861 aaaatgtaat accggcgtat taccacgtac gcgggcaagc gaaaaaagct ataacgcttc
     1921 ccggccgaca ggcggcccgg aatccacagg ggcatgcagg ttctcttcag taacctgcgc
     1981 cattaaatca aaaaggtcat attcgccggg aagctgcgta tcagtcgaat ccagttgttc
     2041 atcatattca gatggcatgg ggtgatatcc agtagctgag aggttgttag cgggtttctg
     2101 ggcgcagccc tgaaccagtc gagtagcact agcggagtgt atacgggctc aatatgctac
     2161 ggtggagtaa cacgttatga aagtgcttca tgtgacagag gaaagtgcag cggcggggcg
     2221 tacgggagaa aatggaagcc cggggatatg acgcctcctc gctcactcag tcgctacgct
     2281 cctgccgttc ggctgcggcg ggcgttacct gcactcacac aacaagctca tgatgaatcc
     2341 acagattcag ggaataaggc gccacacaac aaaggccgcg ccagcggcgc tttttccata
     2401 ggctccgccc ccctgacaag catcacgaaa tctgacgctc aaatcagtgg tggcgaaacc
     2461 cgacaggact ataaagatac caggcgtttc cccctggtgg ctccctcgtg cgctctcctg
     2521 ttcctgcctt tcggtttacc ggtgtcattc cgctgttatg gccgcgttta tctcattcca
     2581 cgcctgacac tcagttccgg gtaggcagtt cgctccaagc tggactgtat gcacgaaccc
     2641 cccgttcagt ccgactgcta cgcctttccg gtaactttca acttgattcc aacccggaaa
     2701 aacacgacga ggcgccactg gcagcagcca ttggtaacag ggttcacgga gcttgattac
     2761 gcactttagt gtgcaagagt tcttgaagtg gcggcctgac tacggctaca ctgaaaggac
     2821 agtatttggt atctgcgctc cgtgaatagc cagttacctt ggtttagtaa gttccccaac
     2881 ctactaaacc gttgaaaaaa ccgcctcccc aggcggtttt ttcttttctg tcgctagact
     2941 acgccgccac ccaaacgatc gtcaaggatc ttccccctct ttgacgacct caacgcaaaa
     3001 ccacctttag atataacttc tttttttaaa agaaaaacag atttcatcca ctattttaat
     3061 agccatgttc cggcataaga gatggcaaaa atgacattcg gcgaaaaaat aatctaattt
     3121 atacaaatat ttatatgtca cctctttaat ttcagaatat gcccaggtta tacttcctag
     3181 gttaaattgg gtcagagcac cctgaaattc atggctctgg caaacactaa acaatcgagg
     3241 gtttatgtat gaacacctta atctaaacga gtgcaggagg atttatggca caactagaat
     3301 tgaaaatgga gaaagttgta gagaaggaat ttcgcgcact agaaaacagg aaggtgcaag
     3361 aggcttttgc tgtagacctc gaaatgataa tgaacgggct caaaccgttg tcatcatcaa
     3421 agccactaaa tggattagga aaaggagttt ttgaactaaa gaaaaacggc cgcccggctt
     3481 acagatgtgt ttatgtagta aaaaacaaca cactatacgt ccttcacgta tacagtaaga
     3541 catcggacgg cacaccaaag catcacgaag acacaataaa aaaacgtttt aaatcagtaa
     3601 aataaataat taaattacgc aaggcggttc tcacacaacc gcctttttta cgctcacatg
     3661 caaaggactt tcttcatcat gcggccgaaa ggtcacatcc acaacaaatc caatgcggca
     3721 cagcatctca aggagcgtat caatggcaaa cttggataca tgcccattca ttaagttact
     3781 aacgcggggc tgactaactc caagcttatc cgcagcagcc gcttgcgacc aaccctcgcc
     3841 tctgatcatt tcagcgatga ttataagcag ctttgatttc aggctgagca tgttcaactc
     3901 aactgcgtct ttagcaaaga gttcaaacgg actgctaaat ttatttagca tacaaatcct
     3961 cctcttcgtc tatgcgttgc atgttcatta gaatagagtg gtcaaaaagc actcaatcca
     4021 catctcatgg gcgctgtatt atacgcaata cacgccccag tgcaagatat ataagtatat
     4081 atatagacac t
//
