LOCUS       NZ_CP086438             3541 bp    DNA     circular CON 28-MAY-2024
DEFINITION  Klebsiella pneumoniae strain AE-2247421-T5-ESBL plasmid
            p2247421-T5-ESBL_7, complete sequence.
ACCESSION   NZ_CP086438
VERSION     NZ_CP086438.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN22108733
            Assembly: GCF_022759945.1
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  JOURNAL   Unpublished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                   :: 269x
            Sequencing Technology :: Illumina NovaSeq; Oxford Nanopore MiniION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_022759945.1-RS_2024_05_28
            Annotation Date                   :: 05/28/2024 04:47:14
            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)                     :: 5,915
            CDSs (total)                      :: 5,794
            Genes (coding)                    :: 5,632
            CDSs (with protein)               :: 5,632
            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)              :: 162
            CDSs (without protein)            :: 162
            Pseudo Genes (ambiguous residues) :: 0 of 162
            Pseudo Genes (frameshifted)       :: 61 of 162
            Pseudo Genes (incomplete)         :: 97 of 162
            Pseudo Genes (internal stop)      :: 28 of 162
            Pseudo Genes (multiple problems)  :: 20 of 162
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP086438.1.
            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-T5-ESBL"
                     /isolation_source="stool"
                     /host="Homo sapiens"
                     /db_xref="taxon:573"
                     /plasmid="p2247421-T5-ESBL_7"
                     /geo_loc_name="Switzerland"
                     /collection_date="2013"
                     /collected_by="Institute for Infectious Diseases Bern"
     gene            join(3156..3541,1..508)
                     /locus_tag="LNN54_RS29455"
                     /old_locus_tag="LNN54_29465"
     CDS             join(3156..3541,1..508)
                     /locus_tag="LNN54_RS29455"
                     /old_locus_tag="LNN54_29465"
                     /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="endonuclease"
                     /protein_id="WP_032419557.1"
                     /translation="MELNLCWWNIGISPPVKGVKKDKAEAIRLAKHYIKKMSQEKTLDF
                     LGICEISEDEAIDFKPLADKLHLEYLNLSGTVGRIIMDVSIMYEASKLEYIDYKYIIKI
                     QPDDRTLRIAVRVVFKDAVTGNLITFFLSHWPSIRSADEKIREDAAESLRNNVNKILDD
                     HGIESQIICMGDYNTNPYSVAINEKLYATRDYHRIKNKRKLLFNPFWYLLSDKKTNNLG
                     TYHYKSGASNRWFVFDQMLFSSSFIYGGKDCLKLDMNSLDFHRILSDDNQCLDQRFFNT
                     FDHYPIFCRIYHDNQK"
                     /name="endonuclease"
     gene            492..929
                     /locus_tag="LNN54_RS29460"
                     /old_locus_tag="LNN54_29470"
     CDS             492..929
                     /locus_tag="LNN54_RS29460"
                     /old_locus_tag="LNN54_29470"
                     /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(1739..2140)
                     /locus_tag="LNN54_RS29465"
                     /old_locus_tag="LNN54_29475"
     CDS             complement(1739..2140)
                     /locus_tag="LNN54_RS29465"
                     /old_locus_tag="LNN54_29475"
                     /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(2140..2331)
                     /locus_tag="LNN54_RS29470"
                     /old_locus_tag="LNN54_29480"
     CDS             complement(2140..2331)
                     /locus_tag="LNN54_RS29470"
                     /old_locus_tag="LNN54_29480"
                     /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            2745..2858
                     /locus_tag="LNN54_RS29475"
                     /old_locus_tag="LNN54_29485"
     CDS             2745..2858
                     /locus_tag="LNN54_RS29475"
                     /old_locus_tag="LNN54_29485"
                     /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"
     Typing          2453..2858
                     /name="ColRNAI_rep_cluster_1987"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="93.643"
                     /coverage="99.0"
                     /evalue="4.5799999999999997e-172"
ORIGIN
        1 attcttttta tcacactggc catccataag aagcgcagat gaaaagattc gagaggacgc
       61 tgccgagtca ctgcgcaaca atgtgaataa aatactagat gaccacggca ttgagtccca
      121 aataatatgc atgggtgatt acaacacaaa cccttactct gttgcaataa acgaaaaact
      181 ttacgccact agagattacc atcgaataaa gaataaacga aaacttcttt ttaacccttt
      241 ttggtattta ctttcagaca aaaagaccaa taacttagga acttatcatt ataaatcagg
      301 agcatcgaat agatggtttg tttttgatca aatgttgttt tcatcatcat ttatatacgg
      361 aggaaaagat tgtcttaagc tagacatgaa cagccttgat tttcatcgta tacttagtga
      421 tgataaccaa tgtttagatc aaagattttt taacactttt gatcattacc caatattttg
      481 taggatttac catgacaacc aaaaatgaag agttccaaga aagactaaag gcatcactaa
      541 aaaaagccaa tgaaacacta attttaaaag aaaaaataga gtcagatatt tcatcaattt
      601 tgtcaatgct aaagggtata acatccgact caattgactt tgatattttt cagaatagtt
      661 cgaaaattcc caaatataaa gattgtaaaa aaattgtcag aataaagaaa aactctagca
      721 tggcataccc taaaggtttc attttatttg gatttagcat aaatgagtct accggatatc
      781 ctgtacaggt agaaacggaa gacgaagccg cagagtgtac agatgtggat aacttaaaag
      841 aatcaattgt ttacataata gaaaaaagat ctatagagat aatgaaatta atatccgagc
      901 aacaagaaga cgatgacatt cctttttaaa aaggtagcat gtaatgccat tatcaacggc
      961 actttttcat agaaggtgcc atatatctta gaatcaacta atttaacata agaccataat
     1021 tgtacgcacc gctaaaacgg cctcagggcg tttctgacgg gaaaccggta aaacaggcaa
     1081 caaaccaccc gaaaacccgc cagaaacgcg caggctctgt ttttacggca tgcatgagta
     1141 tgcacgcaag tgcatagcgc gaaaattcac gccattcagc cagggtaagt cctgtttccg
     1201 gcgttcttcc catccgaaaa cggtgaacgg ggacgcaatt tattgcgtgg ccgtgaagcg
     1261 ttgccggcgc agccggaaaa ccggttttca gcacgttcag gaatcgggtt cgtcgacggc
     1321 cggcaatcac gttatggcaa gtcgccggac gactcaccac acgattcacc ggcgactctt
     1381 cactagagtc gtacccagag tcgccgcgtc taaaaaacaa ccaaacgggg agtcgtgtcc
     1441 agagtcgggt cgttattaac tcattgtttt tatagtcctg agtcgttacc gactctatga
     1501 cgactcgccg gggactctat gacgagtcgt catagagtcg gatctatgta aataaaattt
     1561 aaaaaacgaa atttcaggaa agtaaacaac tgatattaaa tacaaatctg caaaatttta
     1621 attttgcgta gtgtgtgggt atttttagtc gtgaggagcg ttcagagatc tggcgatttt
     1681 tgggaaggtt caggaactcc ccgggatggc cggagaggaa aactcaagca tggcaggatc
     1741 aggatttttt ccagaatttc caccatggtg ccggggattc cgttaatttt gcctggtgat
     1801 tttcaagaag gagcatggcc tgtttcaggc tgtcaatgtg cgaatccttg gacaaaagta
     1861 aggtattcag gtgttcaatc tcctgtttca gatgacgaat cacctgttca ctctggtcag
     1921 cagaggctgt atcacgctgt tcagagacct gtccagaatg gtgttcaccc ttcggttgtt
     1981 caaagggacc aaagacacgt aaaagctctg aagtatctac catttttgca tttcgttcac
     2041 cgctacaggt ggacaggtca cctgctttaa ttaacctgtg cagtgttgtt ctactcttac
     2101 ccgtcagtcg ggcagcctca ctaatagaca ctctggccat cagttaccat cctgtaatgc
     2161 atccagtctc gaggacagtg tacggaaaag atgctccgca tcatcgtgga gtttctcaca
     2221 aaggtcggcc tcgacatcaa gatcaagctc gttaagcttc tccagcagga gcagagactg
     2281 attctggatg aatttagcca tgttcagcgc tgttttctgt tgtttcgtca taagaagcct
     2341 cagagcgtca gtgctcagtg taagaacagt ctcttttccg cttcctcgct cactcagtcg
     2401 ctacgctccg gtcgttcggc tgcggcgagc ggcaggagca tgcgtataaa agctcgagaa
     2461 gaccgagcgg tcaaatgggg aagaaggaaa ggccgcaaag cggccgtttt tccataggct
     2521 ccgcccccct gacaagcatc accgaagcgg acgctcaaat cagtggtggc gaaacccgac
     2581 aggactataa agataccagg cgtttccccc tgatggctcc ctcgtgcgct ctcctgttcc
     2641 tgccattcgg tttaccggtg tcattccgct gttatggccg cgtttttctc attccacgcc
     2701 tgacactcag ttccgggtag gcagttcgct ccaagctgga ctgtatgcac gaaccccccg
     2761 ttcagtccga ctgctgcgcc ttatccggta actatcatct tgagtccaac ccgaaaagac
     2821 acgacaaagc gccactggca gcagccactg gtaactgatt tagaggagtt agtcttgaag
     2881 ttatgggtca gttaaggcta cactgaaaga acaagttttg gtgactgcgc tcctctacta
     2941 gccagttacc taggttcaaa agacctgcaa gttatttgaa cccttgaaaa aaccgccctg
     3001 caaggcggtt ttttcatttc cagccaagaa gataacgcct taaaaggggt agcgcaacac
     3061 catttatcaa caaacagata aataaaatgt ttaaccccca catcaaaagc aatacaataa
     3121 acccaatgaa tacaatgcat taagaaagaa acaccatgga attgaattta tgttggtgga
     3181 atattggaat atcaccacct gtaaaaggcg tgaagaaaga caaggctgag gctattagat
     3241 tggccaagca ctatataaaa aaaatgtctc aagaaaaaac attggatttt ttgggtatct
     3301 gtgaaatatc agaagatgag gctatagatt ttaaaccttt ggctgataaa ctacatcttg
     3361 aatacttgaa tttatcaggg actgttggtc ggataattat ggatgtatcc ataatgtacg
     3421 aagcatcaaa acttgagtac atagattata aatatataat taaaatacaa ccagatgata
     3481 gaactttgcg tattgctgtc agagttgttt ttaaggatgc agtaacagga aatctaataa
     3541 c
//
