LOCUS       NZ_CP086452             5359 bp    DNA     circular CON 28-MAY-2024
DEFINITION  Klebsiella pneumoniae strain AE-2247421-T0 plasmid p2247421-T0_5,
            complete sequence.
ACCESSION   NZ_CP086452
VERSION     NZ_CP086452.1
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 5359)
  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  JOURNAL   Unpublished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 5359)
  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
            CP086452.1.
            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..5359
                     /organism="Klebsiella pneumoniae"
                     /mol_type="genomic DNA"
                     /strain="AE-2247421-T0"
                     /isolation_source="stool"
                     /host="Homo sapiens"
                     /db_xref="taxon:573"
                     /plasmid="p2247421-T0_5"
                     /geo_loc_name="Switzerland"
                     /collection_date="2013"
                     /collected_by="Institute for Infectious Diseases Bern"
     gene            join(5255..5359,1..312)
                     /locus_tag="LNN40_RS29570"
                     /old_locus_tag="LNN40_29575"
     CDS             join(5255..5359,1..312)
                     /locus_tag="LNN40_RS29570"
                     /old_locus_tag="LNN40_29575"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001283459.1"
                     /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_032419562.1"
                     /translation="MSDQKNNLDIQKQTLESKWGKEALSMGWSAIPTSLFFLQGALNMT
                     PTTFNVLLHLIIHWWKPYDWPHPSQESIAVRMGVSSRTVQRSLQELENYGLLTKIRTSK
                     DNPKYKGRNIYDMSLLVKSLNILTPDLNAKLNEK"
                     /name="helix-turn-helix domain-containing protein"
     gene            730..993
                     /locus_tag="LNN40_RS29575"
                     /old_locus_tag="LNN40_29580"
     CDS             730..993
                     /locus_tag="LNN40_RS29575"
                     /old_locus_tag="LNN40_29580"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_010891192.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_054175658.1"
                     /translation="MAAYTSETEKFLQSVSSDQTWWKSRYNPGDSVPHSGIYRCTVCGK
                     EITSNGSDPFPPQNHHQHSQQQAIKWQLIVRTDTKGDRFGIK"
                     /name="hypothetical protein"
     gene            complement(1543..1755)
                     /locus_tag="LNN40_RS29580"
                     /old_locus_tag="LNN40_29585"
     CDS             complement(1543..1755)
                     /locus_tag="LNN40_RS29580"
                     /old_locus_tag="LNN40_29585"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000137423.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MbeD family mobilization/exclusion protein"
                     /protein_id="WP_000137423.1"
                     /translation="MTELEKQLLTALEQLHQDYSQRLDEWESAFAEWQKMSGLMQRENA
                     ALNERVTRLSQQVANLSRQLQRLSQ"
                     /name="MbeD family mobilization/exclusion protein"
     gene            complement(1759..2244)
                     /locus_tag="LNN40_RS29585"
                     /old_locus_tag="LNN40_29590"
     CDS             complement(1759..2244)
                     /locus_tag="LNN40_RS29585"
                     /old_locus_tag="LNN40_29590"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001749519.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MbeB family mobilization protein"
                     /protein_id="WP_064147840.1"
                     /translation="MSSLLALAKDLEQQSKAQQQSTGEMLKAAFSEHEKSVKAELSASA
                     KRISDAISAHEQGMTAAMQSNRLSVLRMVGRTWLTITLVSVLLIATSGSILWWQGQQIT
                     GNYRTIRAQERTQAMLSEKNHGVQLSLCGEKKLSCVKVNPKAGAYGEDGNWMVLERK"
                     /name="MbeB family mobilization protein"
     gene            complement(<2282..2959)
                     /locus_tag="LNN40_RS29805"
                     /old_locus_tag="LNN40_29595"
                     /pseudo=""
     CDS             complement(<2282..2959)
                     /locus_tag="LNN40_RS29805"
                     /old_locus_tag="LNN40_29595"
                     /inference="COORDINATES: protein motif:HMM:NF015397.4"
                     /note="incomplete; partial in the middle of a contig;
                     missing C-terminus; Derived by automated computational
                     analysis using gene prediction method: Protein Homology."
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="relaxase/mobilization nuclease domain-containing
                     protein"
                     /name="relaxase/mobilization nuclease domain-containing
                     protein"
     gene            complement(2922..3242)
                     /locus_tag="LNN40_RS29595"
                     /old_locus_tag="LNN40_29600"
     CDS             complement(2922..3242)
                     /locus_tag="LNN40_RS29595"
                     /old_locus_tag="LNN40_29600"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000957083.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MobC family plasmid mobilization relaxosome
                     protein"
                     /protein_id="WP_042863636.1"
                     /translation="MLTMWVTEDEHRRLLERCDGRQLAAWMRQTCLDEKPARAGRLPSI
                     SPALLRQLAGMGNNLNQIARKVNAGGAGHDRVQIVAALMAIDAGLERLRHAVLEKGGDD
                     DR"
                     /name="MobC family plasmid mobilization relaxosome protein"
     gene            complement(4233..4907)
                     /locus_tag="LNN40_RS29600"
                     /old_locus_tag="LNN40_29605"
     CDS             complement(4233..4907)
                     /locus_tag="LNN40_RS29600"
                     /old_locus_tag="LNN40_29605"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001259273.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="NYN domain-containing protein"
                     /protein_id="WP_032419561.1"
                     /translation="MRTIVYVDGFNFYHGLVKRSGYKWLDLYKLFEEQLLPIRARESQL
                     IQVKFFTAEIKAKFASRGELAHQAQQAYHRALVQIYGDKLQIIKGYYSERQECAMTFNE
                     GHPPSKTDRTTVWKLEEKQTDVRMALEMYRDAIRGEVEQLVLCTNDSDMIPPIEMIKAD
                     RPELKIGIVVPREQDTSRVISNLASLGDWSLPYVSYEALRLALLPDKVPTRRKPILKPN
                     HW"
                     /name="NYN domain-containing protein"
     Typing          complement(3351..3531)
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="87.978"
                     /coverage="83.0"
                     /evalue="2.08e-53"
     Typing          3481..3991
                     /name="ColRNAI_rep_cluster_1987"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="93.359"
                     /coverage="98.0"
                     /evalue="0.0"
     Typing          complement(1428..2932)
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="94.622"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 ttcttcctgc agggcgcact caatatgacc cccacaacat tcaatgtgct acttcatcta
       61 attatccact ggtggaaacc ctatgattgg ccacatccat ctcaagagag catcgcggtt
      121 agaatgggag tttcatcaag aacagttcaa cgctcactcc aagaacttga aaattacgga
      181 ttgcttacaa aaattcgtac aagcaaggac aaccctaagt acaaagggcg aaacatttac
      241 gatatgtctc ttttagttaa gtcactaaac attcttacgc cagacctcaa cgccaaacta
      301 aacgaaaagt aaccaaaaat tccgacagcc aaagcgcgca catcactgta caaaaggtgt
      361 tcagcatcac atttctagaa aatgacaaca gctccctatt gaaagctaat ttctaaacta
      421 aacatcagta tcgctacaca aacagcaata cggacaaaac acaaaaagag gaattagcat
      481 gtctaaagca ccaattggta cgactgcttc taccggacaa aagtgtcctg aaagtggtgt
      541 ctggaaagtc gtaggaaccc cttccactac agccccgata gcaaaaggta atgtaatgcc
      601 tccgtacgca ggaaaggctg taacctggat gttaacccaa tatgcttgat atttagactg
      661 gcaacgaaaa gccgccccag cgggcggctt ttctatctct gccctataaa ttcagaaaag
      721 gaaagctaaa tggctgcata taccagcgaa acagagaagt ttttacaaag cgtcagtagc
      781 gatcaaacat ggtggaagtc acgatataat ccaggagaca gcgttcccca ttctggaatt
      841 tatcgatgta ccgtctgcgg aaaagagatc accagtaacg gcagcgaccc gttcccgccg
      901 caaaaccatc atcagcacag tcagcaacaa gcaatcaaat ggcaattgat tgtcagaacg
      961 gacactaaag gtgaccgttt cggaatcaaa tgattgagag ccctccgggg ctttttttgt
     1021 acctgaagct cgaagatatt taccataaca tcccttgccc gcaccgctcc ggacaggttc
     1081 gccacaaacg ggacggcagt caggtaaaac cggcaacaaa ccacccgata caccgccccg
     1141 ttcgtgacag ataaattttc cccggctgca tggtcatgca gccagatgca tacagtctga
     1201 tttcaggcca gaatccggat gaacgcctta aaaacaggaa aatgcttctc cagccagtcc
     1261 cacagctcgg tcgccagata caggcagtta agtacagctt caatgacgtt aagcaatttc
     1321 ataattcccc ctaggtatag gccgtgctct ttttgatcac gaacctattt agcgggagaa
     1381 ataagagccc ttcttcgtgc ggcctgtcac cggatgatac tgttcagccc agtgtcggac
     1441 cgtcataact ccgctgacgg gaacgggctt ccgccagctc tttttcgtgc tgtcgctgct
     1501 cgtatgcccg ttcggcggcc accgccattt catgccgctg cactactggc tcaaacgctg
     1561 taactgcctg ctcaagttcg ccacctgctg actcaagcgc gtcacgcgct cgttcagtgc
     1621 cgcgttctcc cgttgcataa gcccagacat cttctgccat tccgcgaagg cgctctccca
     1681 ctcgtccagc ctttgcgagt agtcctgatg tagctgctct aatgcggtca gcaactgttt
     1741 ttccagttcc gtcatgggct atttcctctc cagtaccatc cagttcccgt cctccccgta
     1801 agctcccgct ttcgggttca ctttgacgca ggacagtttc ttctccccgc agagcgacag
     1861 ctgcacgccg tggttcttct ccgacagcat ggcctgcgtc cgctcctgcg cccggatagt
     1921 ccggtaattc ccggtgatct gctgcccctg ccaccacaga atgctcccgc tcgtggcgat
     1981 cagcagtacc gagaccaggg tgatggtcag ccacgtccgg ccgaccatac gcagcacgct
     2041 caggcggttc gactgcatcg ccgcggtcat accctgctcg tgggcgctga tggcgtcgct
     2101 gattctcttc gcgcttgcgc tcagttccgc ttttacagat ttctcgtgct cgctgaatgc
     2161 ggctttcagc atctcgccgg tactctgctg ctgcgctttc gattgctgct ccaagtcctt
     2221 cgccagcgct aaaagactgc tcataaatgg ctcccttcag tcggatgttt cgccccccgt
     2281 ccgggtcggc aatgctgata ctgttttttg tggtgcggac cacctcaaaa cctgccgctg
     2341 tgagcgcccc tgtgacgtcc tcgcgcgttt tgagctcccc ggatgaggct aaggccagca
     2401 acccccgtgt aatcgcctga gcggcttcca gcttcgtttc cggcagtgcg gacggcgtga
     2461 ccagtaaccg ccggttctcc ggggcgtttg gatcatgcag ccccagtctg ccgttcacca
     2521 cggtctgcca ggcatcgatg cgcggccggt cggcgcgatc gtagtacggc tgcaggcgtt
     2581 tcccggtcag cagttcagtg ttggggatca ggaaattcag ctccagcctc cccttgtcgg
     2641 tatgctccac ccacagaatg ctgtactggt ctttatcgag cccgggcatc agaacccgct
     2701 caaagctggc catgatctgc tcccgctgcc cgggcggcag ttcagcctcc gcgaacgaca
     2761 gcacgccgga ggtgtacttt ttcgcatacg gcgaggcatc gataagctcc cggacttcct
     2821 ccggttttcc ctgcagcacg gtcgccccct cgcgctgccg gtcttttccc agcaggtaat
     2881 ccaccggacc ggcaccacca ccgcgccccc gggggtgaaa tttaacgatc atcatccccc
     2941 cctttttcca gcaccgcatg ccgcagccgc tccagtcccg cgtcgattgc catcagggcg
     3001 gccacaatct gcacccggtc atgaccggca ccaccggcat tcactttccg ggcgatctgg
     3061 ttcaggttgt tccccatacc ggcaagctgg cgcagcagcg ccggcgatat cgacggcagt
     3121 ctgccggcac gcgccggctt ctcatcgagg caggtctgac gcatccacgc cgccagctgc
     3181 ctgccgtcgc accgctcgag cagccgccgg tgttcgtctt ccgtcaccca catcgtgagc
     3241 atcttgttgc gtttgtctgc cagagtagcc tcctgagaac accgggacgg gcgggaaatg
     3301 tttcccggtc ggcacggtgt tggacaagcc gcaggcgcgt cagtggcttt tagcgggttt
     3361 cggggcgcag ccctgaacca gtcacgtagc gctagcggag tgtatactgg ctcaatatgt
     3421 tacggaggag taacacttta tgaaagtgct tcatgtgaca gggggaaaat gcagctacag
     3481 ggcgtacagg agaaaatgga ggttacggtg atatgacgcc tcctcgctca ctcggtcgct
     3541 tccgctcctg ccgttcggct gcggcgggcg ttacgcacac acggataaga gcaaaggcat
     3601 atgacatgac aagcagggcg ggaaaaggat gcggcgctgc cgtttttcca taggctccgc
     3661 ccccctgaca agcatcacga aatctgacgc tcaaatcagt ggtggcgaaa cccgacagga
     3721 ctataaagat accaggcgtt tccccctggt ggctccctcg tgcgctctcc tgttcctgcc
     3781 tttcggttta ccggtgtcat tccgctgtta tggccgcgtt tgtctcattc cacgcctgac
     3841 actcagttcc gggtaggcag ttcgctccaa gctggactgt atgcacgaac cccccgttca
     3901 gtccgaccgc tgcgcctttt ccggtaacta tcgtcttgag tccaatccgg aaagacacgc
     3961 aaaaacgcca ctggcagcag ccactggtaa caggattcac ggagcagagt agtagagtgc
     4021 ttctacagag ttcttgaagt ggtggcctga ctgcggctac actggaagga cagttttggt
     4081 atctgcgctc cgtgaaagcc agttaccttc gggaaaaaga gttggtagct cttgattccg
     4141 gcaaacgaac caccgttggt agcggtggtt tttttgtttg cagggcatga gattacgacg
     4201 agagtaaaag gatcacaaga agatccggct gtttaccagt gatttggctt cagtattggc
     4261 ttccgcctag tggggacttt atctggcaat aaagctaatc ttaaggcttc ataggataca
     4321 tatggcaagc tccaatcccc taaactagcc agattactaa tcactcgact agtatcctgt
     4381 tcccttggca ctacgattcc tatttttaac tcaggccgat cagcttttat catttctatt
     4441 ggcggtatca tatctgagtc gttagtgcag agaaccaatt gttctacttc accacgaatc
     4501 gcatcgcgat acatttctaa agccattcta acgtctgtct gcttttcttc taacttccag
     4561 accgttgttc tatccgtttt tgatggagga tgcccctcat taaaggtcat tgcacattcc
     4621 tgacgctctg agtaataacc ttttattatc tgtagcttat cgccatagat ctgtactaat
     4681 gctcgatggt aggcttgctg agcttggtgc gccaattcac cccgagaagc aaactttgcc
     4741 ttgatctcag cagtaaagaa cttcacctga atcaactgtg attctcgtgc tcttatcgga
     4801 agcagttgtt cttcaaagag cttataaagg tctaaccact tatatcccga acgcttaacc
     4861 aatccgtgat aaaaattgaa cccatctacg taaactattg ttctcatttt atttcgcgca
     4921 taaaaaaacc gcctctaagg gcggttttaa caacaaaaac taacgttagc aaacagttta
     4981 agttgtagta cctcagggtt aaaactaacc gagagggcgg tttcaagctc ctgaaggaag
     5041 acgcgtaact taatcgctgc ccacctaaag ggaggtttag agcctcaagg gagctgcgta
     5101 acttaatcgc gctaccaaga ggtgagtgta gattaagtat agttaaatat aatgatatta
     5161 taagcgcact ggtgtcgtac taattatatg aattaattta ccaacctgct aagctgaagt
     5221 cttctaagaa gacttcagct tagcaggttg gtatatgtca gatcaaaaaa ataatttaga
     5281 cattcaaaaa cagacacttg agtctaaatg ggggaaggaa gcgttaagca tgggatggtc
     5341 agccattcct acatccctt
//
