LOCUS       NZ_CP086454             3541 bp    DNA     circular CON 28-MAY-2024
DEFINITION  Klebsiella pneumoniae strain AE-2247421-T0 plasmid p2247421-T0_7,
            complete sequence.
ACCESSION   NZ_CP086454
VERSION     NZ_CP086454.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN22108731
            Assembly: GCF_022760005.1
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  JOURNAL   Unpublished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                   :: 223x
            Sequencing Technology :: Illumina NovaSeq; Oxford Nanopore MiniION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_022760005.1-RS_2024_05_28
            Annotation Date                   :: 05/28/2024 04:59:44
            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)                     :: 5,951
            CDSs (total)                      :: 5,830
            Genes (coding)                    :: 5,656
            CDSs (with protein)               :: 5,656
            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)              :: 174
            CDSs (without protein)            :: 174
            Pseudo Genes (ambiguous residues) :: 0 of 174
            Pseudo Genes (frameshifted)       :: 66 of 174
            Pseudo Genes (incomplete)         :: 104 of 174
            Pseudo Genes (internal stop)      :: 28 of 174
            Pseudo Genes (multiple problems)  :: 20 of 174
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP086454.1.
            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-T0"
                     /isolation_source="stool"
                     /host="Homo sapiens"
                     /db_xref="taxon:573"
                     /plasmid="p2247421-T0_7"
                     /geo_loc_name="Switzerland"
                     /collection_date="2013"
                     /collected_by="Institute for Infectious Diseases Bern"
     gene            complement(join(3447..3541,1..343))
                     /locus_tag="LNN40_RS29630"
                     /old_locus_tag="LNN40_29635"
     CDS             complement(join(3447..3541,1..343))
                     /locus_tag="LNN40_RS29630"
                     /old_locus_tag="LNN40_29635"
                     /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(327..1220)
                     /locus_tag="LNN40_RS29635"
                     /old_locus_tag="LNN40_29640"
     CDS             complement(327..1220)
                     /locus_tag="LNN40_RS29635"
                     /old_locus_tag="LNN40_29640"
                     /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(1518..1631)
                     /locus_tag="LNN40_RS29640"
                     /old_locus_tag="LNN40_29645"
     CDS             complement(1518..1631)
                     /locus_tag="LNN40_RS29640"
                     /old_locus_tag="LNN40_29645"
                     /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            2045..2236
                     /locus_tag="LNN40_RS29645"
                     /old_locus_tag="LNN40_29650"
     CDS             2045..2236
                     /locus_tag="LNN40_RS29645"
                     /old_locus_tag="LNN40_29650"
                     /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            2236..2637
                     /locus_tag="LNN40_RS29650"
                     /old_locus_tag="LNN40_29655"
     CDS             2236..2637
                     /locus_tag="LNN40_RS29650"
                     /old_locus_tag="LNN40_29655"
                     /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(1519..1924)
                     /name="ColRNAI_rep_cluster_1987"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="93.643"
                     /coverage="99.0"
                     /evalue="4.5799999999999997e-172"
ORIGIN
        1 agttatccac atctgtacac tctgcggctt cgtcttccgt ttctacctgt acaggatatc
       61 cggtagactc atttatgcta aatccaaata aaatgaaacc tttagggtat gccatgctag
      121 agtttttctt tattctgaca atttttttac aatctttata tttgggaatt ttcgaactat
      181 tctgaaaaat atcaaagtca attgagtcgg atgttatacc ctttagcatt gacaaaattg
      241 atgaaatatc tgactctatt ttttctttta aaattagtgt ttcattggct ttttttagtg
      301 atgcctttag tctttcttgg aactcttcat ttttggttgt catggtaaat cctacaaaat
      361 attgggtaat gatcaaaagt gttaaaaaat ctttgatcta aacattggtt atcatcacta
      421 agtatacgat gaaaatcaag gctgttcatg tctagcttaa gacaatcttt tcctccgtat
      481 ataaatgatg atgaaaacaa catttgatca aaaacaaacc atctattcga tgctcctgat
      541 ttataatgat aagttcctaa gttattggtc tttttgtctg aaagtaaata ccaaaaaggg
      601 ttaaaaagaa gttttcgttt attctttatt cgatggtaat ctctagtggc gtaaagtttt
      661 tcgtttattg caacagagta agggtttgtg ttgtaatcac ccatgcatat tatttgggac
      721 tcaatgccgt ggtcatctag tattttattc acattgttgc gcagtgactc ggcagcgtcc
      781 tctcgaatct tttcatctgc gcttcttatg gatggccagt gtgataaaaa gaatgttatt
      841 agatttcctg ttactgcatc cttaaaaaca actctgacag caatacgcaa agttctatca
      901 tctggttgta ttttaattat atatttataa tctatgtact caagttttga tgcttcgtac
      961 attatggata catccataat tatccgacca acagtccctg ataaattcaa gtattcaaga
     1021 tgtagtttat cagccaaagg tttaaaatct atagcctcat cttctgatat ttcacagata
     1081 cccaaaaaat ccaatgtttt ttcttgagac atttttttta tatagtgctt ggccaatcta
     1141 atagcctcag ccttgtcttt cttcacgcct tttacaggtg gtgatattcc aatattccac
     1201 caacataaat tcaattccat ggtgtttctt tcttaatgca ttgtattcat tgggtttatt
     1261 gtattgcttt tgatgtgggg gttaaacatt ttatttatct gtttgttgat aaatggtgtt
     1321 gcgctacccc ttttaaggcg ttatcttctt ggctggaaat gaaaaaaccg ccttgcaggg
     1381 cggttttttc aagggttcaa ataacttgca ggtcttttga acctaggtaa ctggctagta
     1441 gaggagcgca gtcaccaaaa cttgttcttt cagtgtagcc ttaactgacc cataacttca
     1501 agactaactc ctctaaatca gttaccagtg gctgctgcca gtggcgcttt gtcgtgtctt
     1561 ttcgggttgg actcaagatg atagttaccg gataaggcgc agcagtcgga ctgaacgggg
     1621 ggttcgtgca tacagtccag cttggagcga actgcctacc cggaactgag tgtcaggcgt
     1681 ggaatgagaa aaacgcggcc ataacagcgg aatgacaccg gtaaaccgaa tggcaggaac
     1741 aggagagcgc acgagggagc catcaggggg aaacgcctgg tatctttata gtcctgtcgg
     1801 gtttcgccac cactgatttg agcgtccgct tcggtgatgc ttgtcagggg ggcggagcct
     1861 atggaaaaac ggccgctttg cggcctttcc ttcttcccca tttgaccgct cggtcttctc
     1921 gagcttttat acgcatgctc ctgccgctcg ccgcagccga acgaccggag cgtagcgact
     1981 gagtgagcga ggaagcggaa aagagactgt tcttacactg agcactgacg ctctgaggct
     2041 tcttatgacg aaacaacaga aaacagcgct gaacatggct aaattcatcc agaatcagtc
     2101 tctgctcctg ctggagaagc ttaacgagct tgatcttgat gtcgaggccg acctttgtga
     2161 gaaactccac gatgatgcgg agcatctttt ccgtacactg tcctcgagac tggatgcatt
     2221 acaggatggt aactgatggc cagagtgtct attagtgagg ctgcccgact gacgggtaag
     2281 agtagaacaa cactgcacag gttaattaaa gcaggtgacc tgtccacctg tagcggtgaa
     2341 cgaaatgcaa aaatggtaga tacttcagag cttttacgtg tctttggtcc ctttgaacaa
     2401 ccgaagggtg aacaccattc tggacaggtc tctgaacagc gtgatacagc ctctgctgac
     2461 cagagtgaac aggtgattcg tcatctgaaa caggagattg aacacctgaa taccttactt
     2521 ttgtccaagg attcgcacat tgacagcctg aaacaggcca tgctccttct tgaaaatcac
     2581 caggcaaaat taacggaatc cccggcacca tggtggaaat tctggaaaaa atcctgatcc
     2641 tgccatgctt gagttttcct ctccggccat cccggggagt tcctgaacct tcccaaaaat
     2701 cgccagatct ctgaacgctc ctcacgacta aaaataccca cacactacgc aaaattaaaa
     2761 ttttgcagat ttgtatttaa tatcagttgt ttactttcct gaaatttcgt tttttaaatt
     2821 ttatttacat agatccgact ctatgacgac tcgtcataga gtccccggcg agtcgtcata
     2881 gagtcggtaa cgactcagga ctataaaaac aatgagttaa taacgacccg actctggaca
     2941 cgactccccg tttggttgtt ttttagacgc ggcgactctg ggtacgactc tagtgaagag
     3001 tcgccggtga atcgtgtggt gagtcgtccg gcgacttgcc ataacgtgat tgccggccgt
     3061 cgacgaaccc gattcctgaa cgtgctgaaa accggttttc cggctgcgcc ggcaacgctt
     3121 cacggccacg caataaattg cgtccccgtt caccgttttc ggatgggaag aacgccggaa
     3181 acaggactta ccctggctga atggcgtgaa ttttcgcgct atgcacttgc gtgcatactc
     3241 atgcatgccg taaaaacaga gcctgcgcgt ttctggcggg ttttcgggtg gtttgttgcc
     3301 tgttttaccg gtttcccgtc agaaacgccc tgaggccgtt ttagcggtgc gtacaattat
     3361 ggtcttatgt taaattagtt gattctaaga tatatggcac cttctatgaa aaagtgccgt
     3421 tgataatggc attacatgct acctttttaa aaaggaatgt catcgtcttc ttgttgctcg
     3481 gatattaatt tcattatctc tatagatctt ttttctatta tgtaaacaat tgattctttt
     3541 a
//
