LOCUS       NZ_CP083020             3541 bp    DNA     circular CON 10-FEB-2024
DEFINITION  Klebsiella pneumoniae strain 6709.15-I plasmid p4-6709.15-I,
            complete sequence.
ACCESSION   NZ_CP083020
VERSION     NZ_CP083020.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN21016534
            Assembly: GCF_021137775.1
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  JOURNAL   Unpublished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                   :: 328.832x
            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 03:02:35
            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)                     :: 5,453
            CDSs (total)                      :: 5,332
            Genes (coding)                    :: 5,190
            CDSs (with protein)               :: 5,190
            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)              :: 142
            CDSs (without protein)            :: 142
            Pseudo Genes (ambiguous residues) :: 0 of 142
            Pseudo Genes (frameshifted)       :: 52 of 142
            Pseudo Genes (incomplete)         :: 81 of 142
            Pseudo Genes (internal stop)      :: 30 of 142
            Pseudo Genes (multiple problems)  :: 16 of 142
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP083020.1.
            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="6709.15-I"
                     /isolation_source="urine"
                     /host="Homo sapiens"
                     /db_xref="taxon:573"
                     /plasmid="p4-6709.15-I"
                     /geo_loc_name="Switzerland"
                     /lat_lon="46.947928 N 7.422277 E"
                     /collection_date="2018"
                     /collected_by="Institute for Infectious Diseases (IFIK),
                     University of Bern, Friedbuehlstrasse 51, 3001 Bern,
                     Switzerland"
     gene            complement(join(3521..3541,1..171))
                     /locus_tag="K9F34_RS27170"
                     /old_locus_tag="K9F34_27135"
     CDS             complement(join(3521..3541,1..171))
                     /locus_tag="K9F34_RS27170"
                     /old_locus_tag="K9F34_27135"
                     /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            585..698
                     /locus_tag="K9F34_RS27175"
     CDS             585..698
                     /locus_tag="K9F34_RS27175"
                     /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            996..1889
                     /locus_tag="K9F34_RS27180"
                     /old_locus_tag="K9F34_27140"
     CDS             996..1889
                     /locus_tag="K9F34_RS27180"
                     /old_locus_tag="K9F34_27140"
                     /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            1873..2310
                     /locus_tag="K9F34_RS27185"
                     /old_locus_tag="K9F34_27145"
     CDS             1873..2310
                     /locus_tag="K9F34_RS27185"
                     /old_locus_tag="K9F34_27145"
                     /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(3120..3521)
                     /locus_tag="K9F34_RS27190"
                     /old_locus_tag="K9F34_27150"
     CDS             complement(3120..3521)
                     /locus_tag="K9F34_RS27190"
                     /old_locus_tag="K9F34_27150"
                     /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"
     Typing          293..698
                     /name="ColRNAI_rep_cluster_1987"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="93.643"
                     /coverage="99.0"
                     /evalue="4.5799999999999997e-172"
ORIGIN
        1 atccagtctc gaggacagtg tacggaaaag atgctccgca tcatcgtgga gtttctcaca
       61 aaggtcggcc tcgacatcaa gatcaagctc gttaagcttc tccagcagga gcagagactg
      121 attctggatg aatttagcca tgttcagcgc tgttttctgt tgtttcgtca taagaagcct
      181 cagagcgtca gtgctcagtg taagaacagt ctcttttccg cttcctcgct cactcagtcg
      241 ctacgctccg gtcgttcggc tgcggcgagc ggcaggagca tgcgtataaa agctcgagaa
      301 gaccgagcgg tcaaatgggg aagaaggaaa ggccgcaaag cggccgtttt tccataggct
      361 ccgcccccct gacaagcatc accgaagcgg acgctcaaat cagtggtggc gaaacccgac
      421 aggactataa agataccagg cgtttccccc tgatggctcc ctcgtgcgct ctcctgttcc
      481 tgccattcgg tttaccggtg tcattccgct gttatggccg cgtttttctc attccacgcc
      541 tgacactcag ttccgggtag gcagttcgct ccaagctgga ctgtatgcac gaaccccccg
      601 ttcagtccga ctgctgcgcc ttatccggta actatcatct tgagtccaac ccgaaaagac
      661 acgacaaagc gccactggca gcagccactg gtaactgatt tagaggagtt agtcttgaag
      721 ttatgggtca gttaaggcta cactgaaaga acaagttttg gtgactgcgc tcctctacta
      781 gccagttacc taggttcaaa agacctgcaa gttatttgaa cccttgaaaa aaccgccctg
      841 caaggcggtt ttttcatttc cagccaagaa gataacgcct taaaaggggt agcgcaacac
      901 catttatcaa caaacagata aataaaatgt ttaaccccca catcaaaagc aatacaataa
      961 acccaatgaa tacaatgcat taagaaagaa acaccatgga attgaattta tgttggtgga
     1021 atattggaat atcaccacct gtaaaaggcg tgaagaaaga caaggctgag gctattagat
     1081 tggccaagca ctatataaaa aaaatgtctc aagaaaaaac attggatttt ttgggtatct
     1141 gtgaaatatc agaagatgag gctatagatt ttaaaccttt ggctgataaa ctacatcttg
     1201 aatacttgaa tttatcaggg actgttggtc ggataattat ggatgtatcc ataatgtacg
     1261 aagcatcaaa acttgagtac atagattata aatatataat taaaatacaa ccagatgata
     1321 gaactttgcg tattgctgtc agagttgttt ttaaggatgc agtaacagga aatctaataa
     1381 cattcttttt atcacactgg ccatccataa gaagcgcaga tgaaaagatt cgagaggacg
     1441 ctgccgagtc actgcgcaac aatgtgaata aaatactaga tgaccacggc attgagtccc
     1501 aaataatatg catgggtgat tacaacacaa acccttactc tgttgcaata aacgaaaaac
     1561 tttacgccac tagagattac catcgaataa agaataaacg aaaacttctt tttaaccctt
     1621 tttggtattt actttcagac aaaaagacca ataacttagg aacttatcat tataaatcag
     1681 gagcatcgaa tagatggttt gtttttgatc aaatgttgtt ttcatcatca tttatatacg
     1741 gaggaaaaga ttgtcttaag ctagacatga acagccttga ttttcatcgt atacttagtg
     1801 atgataacca atgtttagat caaagatttt ttaacacttt tgatcattac ccaatatttt
     1861 gtaggattta ccatgacaac caaaaatgaa gagttccaag aaagactaaa ggcatcacta
     1921 aaaaaagcca atgaaacact aattttaaaa gaaaaaatag agtcagatat ttcatcaatt
     1981 ttgtcaatgc taaagggtat aacatccgac tcaattgact ttgatatttt tcagaatagt
     2041 tcgaaaattc ccaaatataa agattgtaaa aaaattgtca gaataaagaa aaactctagc
     2101 atggcatacc ctaaaggttt cattttattt ggatttagca taaatgagtc taccggatat
     2161 cctgtacagg tagaaacgga agacgaagcc gcagagtgta cagatgtgga taacttaaaa
     2221 gaatcaattg tttacataat agaaaaaaga tctatagaga taatgaaatt aatatccgag
     2281 caacaagaag acgatgacat tcctttttaa aaaggtagca tgtaatgcca ttatcaacgg
     2341 cactttttca tagaaggtgc catatatctt agaatcaact aatttaacat aagaccataa
     2401 ttgtacgcac cgctaaaacg gcctcagggc gtttctgacg ggaaaccggt aaaacaggca
     2461 acaaaccacc cgaaaacccg ccagaaacgc gcaggctctg tttttacggc atgcatgagt
     2521 atgcacgcaa gtgcatagcg cgaaaattca cgccattcag ccagggtaag tcctgtttcc
     2581 ggcgttcttc ccatccgaaa acggtgaacg gggacgcaat ttattgcgtg gccgtgaagc
     2641 gttgccggcg cagccggaaa accggttttc agcacgttca ggaatcgggt tcgtcgacgg
     2701 ccggcaatca cgttatggca agtcgccgga cgactcacca cacgattcac cggcgactct
     2761 tcactagagt cgtacccaga gtcgccgcgt ctaaaaaaca accaaacggg gagtcgtgtc
     2821 cagagtcggg tcgttattaa ctcattgttt ttatagtcct gagtcgttac cgactctatg
     2881 acgactcgcc ggggactcta tgacgagtcg tcatagagtc ggatctatgt aaataaaatt
     2941 taaaaaacga aatttcagga aagtaaacaa ctgatattaa atacaaatct gcaaaatttt
     3001 aattttgcgt agtgtgtggg tatttttagt cgtgaggagc gttcagagat ctggcgattt
     3061 ttgggaaggt tcaggaactc cccgggatgg ccggagagga aaactcaagc atggcaggat
     3121 caggattttt tccagaattt ccaccatggt gccggggatt ccgttaattt tgcctggtga
     3181 ttttcaagaa ggagcatggc ctgtttcagg ctgtcaatgt gcgaatcctt ggacaaaagt
     3241 aaggtattca ggtgttcaat ctcctgtttc agatgacgaa tcacctgttc actctggtca
     3301 gcagaggctg tatcacgctg ttcagagacc tgtccagaat ggtgttcacc cttcggttgt
     3361 tcaaagggac caaagacacg taaaagctct gaagtatcta ccatttttgc atttcgttca
     3421 ccgctacagg tggacaggtc acctgcttta attaacctgt gcagtgttgt tctactctta
     3481 cccgtcagtc gggcagcctc actaatagac actctggcca tcagttacca tcctgtaatg
     3541 c
//
