LOCUS       NZ_CP086430             3541 bp    DNA     circular CON 28-MAY-2024
DEFINITION  Klebsiella pneumoniae strain AE-2247421-T20-MAC plasmid
            p2247421-T20-MAC_7, complete sequence.
ACCESSION   NZ_CP086430
VERSION     NZ_CP086430.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN22108734
            Assembly: GCF_022759965.1
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  JOURNAL   Unpublished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                   :: 238x
            Sequencing Technology :: Illumina NovaSeq; Oxford Nanopore MiniION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_022759965.1-RS_2024_05_28
            Annotation Date                   :: 05/28/2024 04:50:27
            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)                     :: 5,932
            CDSs (total)                      :: 5,811
            Genes (coding)                    :: 5,643
            CDSs (with protein)               :: 5,643
            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)              :: 168
            CDSs (without protein)            :: 168
            Pseudo Genes (ambiguous residues) :: 0 of 168
            Pseudo Genes (frameshifted)       :: 63 of 168
            Pseudo Genes (incomplete)         :: 101 of 168
            Pseudo Genes (internal stop)      :: 28 of 168
            Pseudo Genes (multiple problems)  :: 20 of 168
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP086430.1.
            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-MAC"
                     /isolation_source="stool"
                     /host="Homo sapiens"
                     /db_xref="taxon:573"
                     /plasmid="p2247421-T20-MAC_7"
                     /geo_loc_name="Switzerland"
                     /collection_date="2013"
                     /collected_by="Institute for Infectious Diseases Bern"
     gene            join(3121..3541,1..17)
                     /locus_tag="LNN44_RS29535"
                     /old_locus_tag="LNN44_29540"
     CDS             join(3121..3541,1..17)
                     /locus_tag="LNN44_RS29535"
                     /old_locus_tag="LNN44_29540"
                     /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(827..1228)
                     /locus_tag="LNN44_RS29540"
                     /old_locus_tag="LNN44_29545"
     CDS             complement(827..1228)
                     /locus_tag="LNN44_RS29540"
                     /old_locus_tag="LNN44_29545"
                     /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(1228..1419)
                     /locus_tag="LNN44_RS29545"
                     /old_locus_tag="LNN44_29550"
     CDS             complement(1228..1419)
                     /locus_tag="LNN44_RS29545"
                     /old_locus_tag="LNN44_29550"
                     /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            1833..1946
                     /locus_tag="LNN44_RS29550"
                     /old_locus_tag="LNN44_29555"
     CDS             1833..1946
                     /locus_tag="LNN44_RS29550"
                     /old_locus_tag="LNN44_29555"
                     /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            2244..3137
                     /locus_tag="LNN44_RS29555"
                     /old_locus_tag="LNN44_29560"
     CDS             2244..3137
                     /locus_tag="LNN44_RS29555"
                     /old_locus_tag="LNN44_29560"
                     /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"
     Typing          1541..1946
                     /name="ColRNAI_rep_cluster_1987"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="93.643"
                     /coverage="99.0"
                     /evalue="4.5799999999999997e-172"
ORIGIN
        1 atgacattcc tttttaaaaa ggtagcatgt aatgccatta tcaacggcac tttttcatag
       61 aaggtgccat atatcttaga atcaactaat ttaacataag accataattg tacgcaccgc
      121 taaaacggcc tcagggcgtt tctgacggga aaccggtaaa acaggcaaca aaccacccga
      181 aaacccgcca gaaacgcgca ggctctgttt ttacggcatg catgagtatg cacgcaagtg
      241 catagcgcga aaattcacgc cattcagcca gggtaagtcc tgtttccggc gttcttccca
      301 tccgaaaacg gtgaacgggg acgcaattta ttgcgtggcc gtgaagcgtt gccggcgcag
      361 ccggaaaacc ggttttcagc acgttcagga atcgggttcg tcgacggccg gcaatcacgt
      421 tatggcaagt cgccggacga ctcaccacac gattcaccgg cgactcttca ctagagtcgt
      481 acccagagtc gccgcgtcta aaaaacaacc aaacggggag tcgtgtccag agtcgggtcg
      541 ttattaactc attgttttta tagtcctgag tcgttaccga ctctatgacg actcgccggg
      601 gactctatga cgagtcgtca tagagtcgga tctatgtaaa taaaatttaa aaaacgaaat
      661 ttcaggaaag taaacaactg atattaaata caaatctgca aaattttaat tttgcgtagt
      721 gtgtgggtat ttttagtcgt gaggagcgtt cagagatctg gcgatttttg ggaaggttca
      781 ggaactcccc gggatggccg gagaggaaaa ctcaagcatg gcaggatcag gattttttcc
      841 agaatttcca ccatggtgcc ggggattccg ttaattttgc ctggtgattt tcaagaagga
      901 gcatggcctg tttcaggctg tcaatgtgcg aatccttgga caaaagtaag gtattcaggt
      961 gttcaatctc ctgtttcaga tgacgaatca cctgttcact ctggtcagca gaggctgtat
     1021 cacgctgttc agagacctgt ccagaatggt gttcaccctt cggttgttca aagggaccaa
     1081 agacacgtaa aagctctgaa gtatctacca tttttgcatt tcgttcaccg ctacaggtgg
     1141 acaggtcacc tgctttaatt aacctgtgca gtgttgttct actcttaccc gtcagtcggg
     1201 cagcctcact aatagacact ctggccatca gttaccatcc tgtaatgcat ccagtctcga
     1261 ggacagtgta cggaaaagat gctccgcatc atcgtggagt ttctcacaaa ggtcggcctc
     1321 gacatcaaga tcaagctcgt taagcttctc cagcaggagc agagactgat tctggatgaa
     1381 tttagccatg ttcagcgctg ttttctgttg tttcgtcata agaagcctca gagcgtcagt
     1441 gctcagtgta agaacagtct cttttccgct tcctcgctca ctcagtcgct acgctccggt
     1501 cgttcggctg cggcgagcgg caggagcatg cgtataaaag ctcgagaaga ccgagcggtc
     1561 aaatggggaa gaaggaaagg ccgcaaagcg gccgtttttc cataggctcc gcccccctga
     1621 caagcatcac cgaagcggac gctcaaatca gtggtggcga aacccgacag gactataaag
     1681 ataccaggcg tttccccctg atggctccct cgtgcgctct cctgttcctg ccattcggtt
     1741 taccggtgtc attccgctgt tatggccgcg tttttctcat tccacgcctg acactcagtt
     1801 ccgggtaggc agttcgctcc aagctggact gtatgcacga accccccgtt cagtccgact
     1861 gctgcgcctt atccggtaac tatcatcttg agtccaaccc gaaaagacac gacaaagcgc
     1921 cactggcagc agccactggt aactgattta gaggagttag tcttgaagtt atgggtcagt
     1981 taaggctaca ctgaaagaac aagttttggt gactgcgctc ctctactagc cagttaccta
     2041 ggttcaaaag acctgcaagt tatttgaacc cttgaaaaaa ccgccctgca aggcggtttt
     2101 ttcatttcca gccaagaaga taacgcctta aaaggggtag cgcaacacca tttatcaaca
     2161 aacagataaa taaaatgttt aacccccaca tcaaaagcaa tacaataaac ccaatgaata
     2221 caatgcatta agaaagaaac accatggaat tgaatttatg ttggtggaat attggaatat
     2281 caccacctgt aaaaggcgtg aagaaagaca aggctgaggc tattagattg gccaagcact
     2341 atataaaaaa aatgtctcaa gaaaaaacat tggatttttt gggtatctgt gaaatatcag
     2401 aagatgaggc tatagatttt aaacctttgg ctgataaact acatcttgaa tacttgaatt
     2461 tatcagggac tgttggtcgg ataattatgg atgtatccat aatgtacgaa gcatcaaaac
     2521 ttgagtacat agattataaa tatataatta aaatacaacc agatgataga actttgcgta
     2581 ttgctgtcag agttgttttt aaggatgcag taacaggaaa tctaataaca ttctttttat
     2641 cacactggcc atccataaga agcgcagatg aaaagattcg agaggacgct gccgagtcac
     2701 tgcgcaacaa tgtgaataaa atactagatg accacggcat tgagtcccaa ataatatgca
     2761 tgggtgatta caacacaaac ccttactctg ttgcaataaa cgaaaaactt tacgccacta
     2821 gagattacca tcgaataaag aataaacgaa aacttctttt taaccctttt tggtatttac
     2881 tttcagacaa aaagaccaat aacttaggaa cttatcatta taaatcagga gcatcgaata
     2941 gatggtttgt ttttgatcaa atgttgtttt catcatcatt tatatacgga ggaaaagatt
     3001 gtcttaagct agacatgaac agccttgatt ttcatcgtat acttagtgat gataaccaat
     3061 gtttagatca aagatttttt aacacttttg atcattaccc aatattttgt aggatttacc
     3121 atgacaacca aaaatgaaga gttccaagaa agactaaagg catcactaaa aaaagccaat
     3181 gaaacactaa ttttaaaaga aaaaatagag tcagatattt catcaatttt gtcaatgcta
     3241 aagggtataa catccgactc aattgacttt gatatttttc agaatagttc gaaaattccc
     3301 aaatataaag attgtaaaaa aattgtcaga ataaagaaaa actctagcat ggcataccct
     3361 aaaggtttca ttttatttgg atttagcata aatgagtcta ccggatatcc tgtacaggta
     3421 gaaacggaag acgaagccgc agagtgtaca gatgtggata acttaaaaga atcaattgtt
     3481 tacataatag aaaaaagatc tatagagata atgaaattaa tatccgagca acaagaagac
     3541 g
//
