LOCUS       NZ_CP083025             3541 bp    DNA     circular CON 10-FEB-2024
DEFINITION  Klebsiella pneumoniae strain 6611.48 plasmid p4-6611.48, complete
            sequence.
ACCESSION   NZ_CP083025
VERSION     NZ_CP083025.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN21016525
            Assembly: GCF_021137795.1
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  JOURNAL   Unpublished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                   :: 229.2595x
            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 03:03:01
            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)                     :: 5,473
            CDSs (total)                      :: 5,352
            Genes (coding)                    :: 5,211
            CDSs (with protein)               :: 5,211
            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)              :: 141
            CDSs (without protein)            :: 141
            Pseudo Genes (ambiguous residues) :: 0 of 141
            Pseudo Genes (frameshifted)       :: 53 of 141
            Pseudo Genes (incomplete)         :: 79 of 141
            Pseudo Genes (internal stop)      :: 30 of 141
            Pseudo Genes (multiple problems)  :: 16 of 141
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP083025.1.
            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="6611.48"
                     /isolation_source="urine"
                     /host="Homo sapiens"
                     /db_xref="taxon:573"
                     /plasmid="p4-6611.48"
                     /geo_loc_name="Switzerland"
                     /lat_lon="46.947928 N 7.422277 E"
                     /collection_date="2017"
                     /collected_by="Institute for Infectious Diseases (IFIK),
                     University of Bern, Friedbuehlstrasse 51, 3001 Bern,
                     Switzerland"
     gene            complement(join(2653..3541,1..5))
                     /locus_tag="K9F27_RS27275"
                     /old_locus_tag="K9F27_27240"
     CDS             complement(join(2653..3541,1..5))
                     /locus_tag="K9F27_RS27275"
                     /old_locus_tag="K9F27_27240"
                     /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(303..416)
                     /locus_tag="K9F27_RS27280"
     CDS             complement(303..416)
                     /locus_tag="K9F27_RS27280"
                     /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            830..1021
                     /locus_tag="K9F27_RS27285"
                     /old_locus_tag="K9F27_27245"
     CDS             830..1021
                     /locus_tag="K9F27_RS27285"
                     /old_locus_tag="K9F27_27245"
                     /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            1021..1422
                     /locus_tag="K9F27_RS27290"
                     /old_locus_tag="K9F27_27250"
     CDS             1021..1422
                     /locus_tag="K9F27_RS27290"
                     /old_locus_tag="K9F27_27250"
                     /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(2232..2669)
                     /locus_tag="K9F27_RS27295"
                     /old_locus_tag="K9F27_27255"
     CDS             complement(2232..2669)
                     /locus_tag="K9F27_RS27295"
                     /old_locus_tag="K9F27_27255"
                     /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          complement(304..709)
                     /name="ColRNAI_rep_cluster_1987"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="93.643"
                     /coverage="99.0"
                     /evalue="4.5799999999999997e-172"
ORIGIN
        1 tccatggtgt ttctttctta atgcattgta ttcattgggt ttattgtatt gcttttgatg
       61 tgggggttaa acattttatt tatctgtttg ttgataaatg gtgttgcgct acccctttta
      121 aggcgttatc ttcttggctg gaaatgaaaa aaccgccttg cagggcggtt ttttcaaggg
      181 ttcaaataac ttgcaggtct tttgaaccta ggtaactggc tagtagagga gcgcagtcac
      241 caaaacttgt tctttcagtg tagccttaac tgacccataa cttcaagact aactcctcta
      301 aatcagttac cagtggctgc tgccagtggc gctttgtcgt gtcttttcgg gttggactca
      361 agatgatagt taccggataa ggcgcagcag tcggactgaa cggggggttc gtgcatacag
      421 tccagcttgg agcgaactgc ctacccggaa ctgagtgtca ggcgtggaat gagaaaaacg
      481 cggccataac agcggaatga caccggtaaa ccgaatggca ggaacaggag agcgcacgag
      541 ggagccatca gggggaaacg cctggtatct ttatagtcct gtcgggtttc gccaccactg
      601 atttgagcgt ccgcttcggt gatgcttgtc aggggggcgg agcctatgga aaaacggccg
      661 ctttgcggcc tttccttctt ccccatttga ccgctcggtc ttctcgagct tttatacgca
      721 tgctcctgcc gctcgccgca gccgaacgac cggagcgtag cgactgagtg agcgaggaag
      781 cggaaaagag actgttctta cactgagcac tgacgctctg aggcttctta tgacgaaaca
      841 acagaaaaca gcgctgaaca tggctaaatt catccagaat cagtctctgc tcctgctgga
      901 gaagcttaac gagcttgatc ttgatgtcga ggccgacctt tgtgagaaac tccacgatga
      961 tgcggagcat cttttccgta cactgtcctc gagactggat gcattacagg atggtaactg
     1021 atggccagag tgtctattag tgaggctgcc cgactgacgg gtaagagtag aacaacactg
     1081 cacaggttaa ttaaagcagg tgacctgtcc acctgtagcg gtgaacgaaa tgcaaaaatg
     1141 gtagatactt cagagctttt acgtgtcttt ggtccctttg aacaaccgaa gggtgaacac
     1201 cattctggac aggtctctga acagcgtgat acagcctctg ctgaccagag tgaacaggtg
     1261 attcgtcatc tgaaacagga gattgaacac ctgaatacct tacttttgtc caaggattcg
     1321 cacattgaca gcctgaaaca ggccatgctc cttcttgaaa atcaccaggc aaaattaacg
     1381 gaatccccgg caccatggtg gaaattctgg aaaaaatcct gatcctgcca tgcttgagtt
     1441 ttcctctccg gccatcccgg ggagttcctg aaccttccca aaaatcgcca gatctctgaa
     1501 cgctcctcac gactaaaaat acccacacac tacgcaaaat taaaattttg cagatttgta
     1561 tttaatatca gttgtttact ttcctgaaat ttcgtttttt aaattttatt tacatagatc
     1621 cgactctatg acgactcgtc atagagtccc cggcgagtcg tcatagagtc ggtaacgact
     1681 caggactata aaaacaatga gttaataacg acccgactct ggacacgact ccccgtttgg
     1741 ttgtttttta gacgcggcga ctctgggtac gactctagtg aagagtcgcc ggtgaatcgt
     1801 gtggtgagtc gtccggcgac ttgccataac gtgattgccg gccgtcgacg aacccgattc
     1861 ctgaacgtgc tgaaaaccgg ttttccggct gcgccggcaa cgcttcacgg ccacgcaata
     1921 aattgcgtcc ccgttcaccg ttttcggatg ggaagaacgc cggaaacagg acttaccctg
     1981 gctgaatggc gtgaattttc gcgctatgca cttgcgtgca tactcatgca tgccgtaaaa
     2041 acagagcctg cgcgtttctg gcgggttttc gggtggtttg ttgcctgttt taccggtttc
     2101 ccgtcagaaa cgccctgagg ccgttttagc ggtgcgtaca attatggtct tatgttaaat
     2161 tagttgattc taagatatat ggcaccttct atgaaaaagt gccgttgata atggcattac
     2221 atgctacctt tttaaaaagg aatgtcatcg tcttcttgtt gctcggatat taatttcatt
     2281 atctctatag atcttttttc tattatgtaa acaattgatt cttttaagtt atccacatct
     2341 gtacactctg cggcttcgtc ttccgtttct acctgtacag gatatccggt agactcattt
     2401 atgctaaatc caaataaaat gaaaccttta gggtatgcca tgctagagtt tttctttatt
     2461 ctgacaattt ttttacaatc tttatatttg ggaattttcg aactattctg aaaaatatca
     2521 aagtcaattg agtcggatgt tatacccttt agcattgaca aaattgatga aatatctgac
     2581 tctatttttt cttttaaaat tagtgtttca ttggcttttt ttagtgatgc ctttagtctt
     2641 tcttggaact cttcattttt ggttgtcatg gtaaatccta caaaatattg ggtaatgatc
     2701 aaaagtgtta aaaaatcttt gatctaaaca ttggttatca tcactaagta tacgatgaaa
     2761 atcaaggctg ttcatgtcta gcttaagaca atcttttcct ccgtatataa atgatgatga
     2821 aaacaacatt tgatcaaaaa caaaccatct attcgatgct cctgatttat aatgataagt
     2881 tcctaagtta ttggtctttt tgtctgaaag taaataccaa aaagggttaa aaagaagttt
     2941 tcgtttattc tttattcgat ggtaatctct agtggcgtaa agtttttcgt ttattgcaac
     3001 agagtaaggg tttgtgttgt aatcacccat gcatattatt tgggactcaa tgccgtggtc
     3061 atctagtatt ttattcacat tgttgcgcag tgactcggca gcgtcctctc gaatcttttc
     3121 atctgcgctt cttatggatg gccagtgtga taaaaagaat gttattagat ttcctgttac
     3181 tgcatcctta aaaacaactc tgacagcaat acgcaaagtt ctatcatctg gttgtatttt
     3241 aattatatat ttataatcta tgtactcaag ttttgatgct tcgtacatta tggatacatc
     3301 cataattatc cgaccaacag tccctgataa attcaagtat tcaagatgta gtttatcagc
     3361 caaaggttta aaatctatag cctcatcttc tgatatttca cagataccca aaaaatccaa
     3421 tgttttttct tgagacattt tttttatata gtgcttggcc aatctaatag cctcagcctt
     3481 gtctttcttc acgcctttta caggtggtga tattccaata ttccaccaac ataaattcaa
     3541 t
//
