LOCUS       NZ_CP086422             3541 bp    DNA     circular CON 28-MAY-2024
DEFINITION  Klebsiella pneumoniae strain AE-2247421-T20-ESBL plasmid
            p2247421-T20-ESBL_6, complete sequence.
ACCESSION   NZ_CP086422
VERSION     NZ_CP086422.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN22108735
            Assembly: GCF_022759985.1
KEYWORDS    RefSeq.
SOURCE      Klebsiella pneumoniae
  ORGANISM  Klebsiella pneumoniae
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Klebsiella/Raoultella group; Klebsiella.
REFERENCE   1  (bases 1 to 3541)
  AUTHORS   Moser,A.I., Endimiani,A., Campos-Madueno,E.I. and Vallone,A.
  TITLE     Genome plasticity in E. coli and K. pneumoniae: SNV accumulation
            over time
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 3541)
  AUTHORS   Moser,A.I., Endimiani,A., Campos-Madueno,E.I. and Vallone,A.
  TITLE     Direct Submission
  JOURNAL   Submitted (04-NOV-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                   :: 299x
            Sequencing Technology :: Illumina NovaSeq; Oxford Nanopore MiniION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_022759985.1-RS_2024_05_28
            Annotation Date                   :: 05/28/2024 04:47:52
            Annotation Pipeline :: NCBI Prokaryotic Genome Annotation Pipeline
            (PGAP)
            Annotation Method :: Best-placed reference protein set; GeneMarkS-2+
            Annotation Software revision      :: 6.7
            Features Annotated                :: Gene; CDS; rRNA; tRNA; ncRNA
            Genes (total)                     :: 5,834
            CDSs (total)                      :: 5,713
            Genes (coding)                    :: 5,548
            CDSs (with protein)               :: 5,548
            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)       :: 63 of 165
            Pseudo Genes (incomplete)         :: 98 of 165
            Pseudo Genes (internal stop)      :: 28 of 165
            Pseudo Genes (multiple problems)  :: 20 of 165
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP086422.1.
            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="AE-2247421-T20-ESBL"
                     /isolation_source="stool"
                     /host="Homo sapiens"
                     /db_xref="taxon:573"
                     /plasmid="p2247421-T20-ESBL_6"
                     /geo_loc_name="Switzerland"
                     /collection_date="2013"
                     /collected_by="Institute for Infectious Diseases Bern"
     gene            complement(join(3477..3541,1..373))
                     /locus_tag="LNN42_RS29050"
                     /old_locus_tag="LNN42_29055"
     CDS             complement(join(3477..3541,1..373))
                     /locus_tag="LNN42_RS29050"
                     /old_locus_tag="LNN42_29055"
                     /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(357..1250)
                     /locus_tag="LNN42_RS29055"
                     /old_locus_tag="LNN42_29060"
     CDS             complement(357..1250)
                     /locus_tag="LNN42_RS29055"
                     /old_locus_tag="LNN42_29060"
                     /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(1548..1661)
                     /locus_tag="LNN42_RS29060"
                     /old_locus_tag="LNN42_29065"
     CDS             complement(1548..1661)
                     /locus_tag="LNN42_RS29060"
                     /old_locus_tag="LNN42_29065"
                     /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            2075..2266
                     /locus_tag="LNN42_RS29065"
                     /old_locus_tag="LNN42_29070"
     CDS             2075..2266
                     /locus_tag="LNN42_RS29065"
                     /old_locus_tag="LNN42_29070"
                     /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            2266..2667
                     /locus_tag="LNN42_RS29070"
                     /old_locus_tag="LNN42_29075"
     CDS             2266..2667
                     /locus_tag="LNN42_RS29070"
                     /old_locus_tag="LNN42_29075"
                     /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          complement(1549..1954)
                     /name="ColRNAI_rep_cluster_1987"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="93.643"
                     /coverage="99.0"
                     /evalue="4.5799999999999997e-172"
ORIGIN
        1 tttctattat gtaaacaatt gattctttta agttatccac atctgtacac tctgcggctt
       61 cgtcttccgt ttctacctgt acaggatatc cggtagactc atttatgcta aatccaaata
      121 aaatgaaacc tttagggtat gccatgctag agtttttctt tattctgaca atttttttac
      181 aatctttata tttgggaatt ttcgaactat tctgaaaaat atcaaagtca attgagtcgg
      241 atgttatacc ctttagcatt gacaaaattg atgaaatatc tgactctatt ttttctttta
      301 aaattagtgt ttcattggct ttttttagtg atgcctttag tctttcttgg aactcttcat
      361 ttttggttgt catggtaaat cctacaaaat attgggtaat gatcaaaagt gttaaaaaat
      421 ctttgatcta aacattggtt atcatcacta agtatacgat gaaaatcaag gctgttcatg
      481 tctagcttaa gacaatcttt tcctccgtat ataaatgatg atgaaaacaa catttgatca
      541 aaaacaaacc atctattcga tgctcctgat ttataatgat aagttcctaa gttattggtc
      601 tttttgtctg aaagtaaata ccaaaaaggg ttaaaaagaa gttttcgttt attctttatt
      661 cgatggtaat ctctagtggc gtaaagtttt tcgtttattg caacagagta agggtttgtg
      721 ttgtaatcac ccatgcatat tatttgggac tcaatgccgt ggtcatctag tattttattc
      781 acattgttgc gcagtgactc ggcagcgtcc tctcgaatct tttcatctgc gcttcttatg
      841 gatggccagt gtgataaaaa gaatgttatt agatttcctg ttactgcatc cttaaaaaca
      901 actctgacag caatacgcaa agttctatca tctggttgta ttttaattat atatttataa
      961 tctatgtact caagttttga tgcttcgtac attatggata catccataat tatccgacca
     1021 acagtccctg ataaattcaa gtattcaaga tgtagtttat cagccaaagg tttaaaatct
     1081 atagcctcat cttctgatat ttcacagata cccaaaaaat ccaatgtttt ttcttgagac
     1141 atttttttta tatagtgctt ggccaatcta atagcctcag ccttgtcttt cttcacgcct
     1201 tttacaggtg gtgatattcc aatattccac caacataaat tcaattccat ggtgtttctt
     1261 tcttaatgca ttgtattcat tgggtttatt gtattgcttt tgatgtgggg gttaaacatt
     1321 ttatttatct gtttgttgat aaatggtgtt gcgctacccc ttttaaggcg ttatcttctt
     1381 ggctggaaat gaaaaaaccg ccttgcaggg cggttttttc aagggttcaa ataacttgca
     1441 ggtcttttga acctaggtaa ctggctagta gaggagcgca gtcaccaaaa cttgttcttt
     1501 cagtgtagcc ttaactgacc cataacttca agactaactc ctctaaatca gttaccagtg
     1561 gctgctgcca gtggcgcttt gtcgtgtctt ttcgggttgg actcaagatg atagttaccg
     1621 gataaggcgc agcagtcgga ctgaacgggg ggttcgtgca tacagtccag cttggagcga
     1681 actgcctacc cggaactgag tgtcaggcgt ggaatgagaa aaacgcggcc ataacagcgg
     1741 aatgacaccg gtaaaccgaa tggcaggaac aggagagcgc acgagggagc catcaggggg
     1801 aaacgcctgg tatctttata gtcctgtcgg gtttcgccac cactgatttg agcgtccgct
     1861 tcggtgatgc ttgtcagggg ggcggagcct atggaaaaac ggccgctttg cggcctttcc
     1921 ttcttcccca tttgaccgct cggtcttctc gagcttttat acgcatgctc ctgccgctcg
     1981 ccgcagccga acgaccggag cgtagcgact gagtgagcga ggaagcggaa aagagactgt
     2041 tcttacactg agcactgacg ctctgaggct tcttatgacg aaacaacaga aaacagcgct
     2101 gaacatggct aaattcatcc agaatcagtc tctgctcctg ctggagaagc ttaacgagct
     2161 tgatcttgat gtcgaggccg acctttgtga gaaactccac gatgatgcgg agcatctttt
     2221 ccgtacactg tcctcgagac tggatgcatt acaggatggt aactgatggc cagagtgtct
     2281 attagtgagg ctgcccgact gacgggtaag agtagaacaa cactgcacag gttaattaaa
     2341 gcaggtgacc tgtccacctg tagcggtgaa cgaaatgcaa aaatggtaga tacttcagag
     2401 cttttacgtg tctttggtcc ctttgaacaa ccgaagggtg aacaccattc tggacaggtc
     2461 tctgaacagc gtgatacagc ctctgctgac cagagtgaac aggtgattcg tcatctgaaa
     2521 caggagattg aacacctgaa taccttactt ttgtccaagg attcgcacat tgacagcctg
     2581 aaacaggcca tgctccttct tgaaaatcac caggcaaaat taacggaatc cccggcacca
     2641 tggtggaaat tctggaaaaa atcctgatcc tgccatgctt gagttttcct ctccggccat
     2701 cccggggagt tcctgaacct tcccaaaaat cgccagatct ctgaacgctc ctcacgacta
     2761 aaaataccca cacactacgc aaaattaaaa ttttgcagat ttgtatttaa tatcagttgt
     2821 ttactttcct gaaatttcgt tttttaaatt ttatttacat agatccgact ctatgacgac
     2881 tcgtcataga gtccccggcg agtcgtcata gagtcggtaa cgactcagga ctataaaaac
     2941 aatgagttaa taacgacccg actctggaca cgactccccg tttggttgtt ttttagacgc
     3001 ggcgactctg ggtacgactc tagtgaagag tcgccggtga atcgtgtggt gagtcgtccg
     3061 gcgacttgcc ataacgtgat tgccggccgt cgacgaaccc gattcctgaa cgtgctgaaa
     3121 accggttttc cggctgcgcc ggcaacgctt cacggccacg caataaattg cgtccccgtt
     3181 caccgttttc ggatgggaag aacgccggaa acaggactta ccctggctga atggcgtgaa
     3241 ttttcgcgct atgcacttgc gtgcatactc atgcatgccg taaaaacaga gcctgcgcgt
     3301 ttctggcggg ttttcgggtg gtttgttgcc tgttttaccg gtttcccgtc agaaacgccc
     3361 tgaggccgtt ttagcggtgc gtacaattat ggtcttatgt taaattagtt gattctaaga
     3421 tatatggcac cttctatgaa aaagtgccgt tgataatggc attacatgct acctttttaa
     3481 aaaggaatgt catcgtcttc ttgttgctcg gatattaatt tcattatctc tatagatctt
     3541 t
//
